##################################
#                                #
# Last modified 2020/06/28       # 
#                                #
# Georgi Marinov                 #
#                                # 
##################################

import sys
import string
import os

Cgenome = '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa'
Cbowtie = '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes'
Pgenome = '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa'
Pbowtie = '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20'
SC3CS = '/oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes'
SCS = '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes'
PCS = '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes'
CCS = '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes'
SCSnoM = '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes'
PCSnoM = '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes'
CCSnoM = '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes'

def run():

    if len(sys.argv) < 1:
        print 'usage: python %s config' % sys.argv[0]
        print '\tconfig format:'
        print '\tlabel\tfastq1\tfastq2\tspecies'
        print '\tspecies key: Candida|S.pombe'
        sys.exit(1)

    config = sys.argv[1]

    DataDict = {}

    linelist = open(config)
    for line in linelist:
        if line.startswith('#'):
            continue
        fields = line.strip().split('\t')
        label = fields[0]
        end1 = fields[1]
        end2 = fields[2]
        species = fields[3]
        DataDict[label] = {}
        DataDict[label]['input'] = (end1,end2,species)
    
    labels = DataDict.keys()
    labels.sort()

    print 'generating countlines.sh'

    outfile = open('countlines.sh','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = 'zcat ' + end1 + ' | wc -l > ' + label + '.fastq.lines'
        outfile.write(outline + '\n')

    outfile.close()

    print 'generating map.sh'
    outfile = open('map.sh','w')

    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ' + end1 
        outline = outline + ' 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie '
        if species == 'S.pombe':
            outline = outline + Pbowtie
        if species == 'Candida':
            outline = outline + Cbowtie
        outline = outline + ' -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT '
        if species == 'S.pombe':
            outline = outline + Pgenome
        if species == 'Candida':
            outline = outline + Cgenome
        outline = outline + ' - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ' + label
        if species == 'S.pombe':
            outline = outline + '.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique'
            DataDict[label]['SEbam'] = label + '.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam'
        if species == 'Candida':
            outline = outline + '.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique'
            DataDict[label]['SEbam'] = label + '.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam'
        outfile.write(outline + '\n')

        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ' + end1 + ' ' + end2
        outline = outline + ' -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie '
        if species == 'S.pombe':
            outline = outline + Pbowtie
        if species == 'Candida':
            outline = outline + Cbowtie
        outline = outline + ' -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT '
        if species == 'S.pombe':
            outline = outline + Pgenome
        if species == 'Candida':
            outline = outline + Cgenome
        outline = outline + ' - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ' + label
        if species == 'S.pombe':
            outline = outline + '.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a'
            DataDict[label]['PEbam'] = label + '.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam'
        if species == 'Candida':
            outline = outline + '.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a'
            DataDict[label]['PEbam'] = label + '.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam'
        outfile.write(outline + '\n')

    outfile.close()

    print 'generating filterchrM.sh'
    outfile = open('filterchrM.sh','w')

    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = '/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view ' + DataDict[label]['SEbam']
        outline = outline + " | egrep -v 'sacCer3_chrM|Candida_glabrata_mito|Schizosaccharomyces_pombe_chrM|Schizosaccharomyces_pombe_MTRSchizosaccharomyces_pombe_AB325691' | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT "
        if species == 'S.pombe':
            outline = outline + Pgenome
            DataDict[label]['SEnochrMbam'] = label + '.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam'
        if species == 'Candida':
            outline = outline + Cgenome
            DataDict[label]['SEnochrMbam'] = label + '.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam'
        outline = outline + ' - -o ' + DataDict[label]['SEnochrMbam']
        outfile.write(outline + '\n')

    outfile.close()

    print 'generating samtools-index.sh'
    outfile = open('samtools-index.sh','w')

    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = '/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools index ' + DataDict[label]['SEnochrMbam']
        outfile.write(outline + '\n')
        outline = '/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools index ' + DataDict[label]['SEbam']
        outfile.write(outline + '\n')
        outline = '/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools index ' + DataDict[label]['PEbam']
        outfile.write(outline + '\n')

    outfile.close()

    print 'generating PEInsertDistFromBAM.sh'
    outfile = open('PEInsertDistFromBAM.sh','w')

    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ' + DataDict[label]['PEbam'] + ' ' + SCS + ' ' + label + '.2x36mers.sacCer3.InsertLength'
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ' + DataDict[label]['PEbam']
        if species == 'S.pombe':
            outline = outline + ' ' + PCS + ' ' + label + '.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.InsertLength'
        if species == 'Candida':
            outline = outline + ' ' + CCS + ' ' + label + '.2x36mers.C_glabrata_CBS138_current_chromosomes.InsertLength'
        outfile.write(outline + '\n')

    outfile.close()

    print 'generating SAMstats.sh'
    outfile = open('SAMstats.sh','w')

    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ' + DataDict[label]['SEnochrMbam'] + ' SAMstats-'
        outline = outline + label + '.1x36mers.sacCer3.unique.nochrM -bam ' + SCS + ' /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired'
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ' + DataDict[label]['PEbam'] + ' SAMstats-'
        outline = outline + label + '.2x36mers.sacCer3 -bam ' + SCS + ' /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired'
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ' + DataDict[label]['PEbam'] + ' SAMstats-'
        outline = outline + label + '.2x36mers.sacCer3.nochrM.ERMTOC -bam ' + SCSnoM + ' /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        if species == 'S.pombe':
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ' + DataDict[label]['SEnochrMbam'] + ' SAMstats-'
            outline = outline + label + '.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam ' + PCS + ' /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired'
            outfile.write(outline + '\n')
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ' + DataDict[label]['PEbam'] + ' SAMstats-'
            outline = outline + label + '.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam ' + PCS + ' /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired'
            outfile.write(outline + '\n')
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ' + DataDict[label]['PEbam'] + ' SAMstats-'
            outline = outline + label + '.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam ' + PCSnoM + ' /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
        if species == 'Candida':
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ' + DataDict[label]['SEnochrMbam'] + ' SAMstats-'
            outline = outline + label + '.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam ' + CCS + ' /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired'
            outfile.write(outline + '\n')
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ' + DataDict[label]['PEbam'] + ' SAMstats-'
            outline = outline + label + '.2x36mers.C_glabrata_CBS138_current_chromosomes -bam ' + CCS + ' /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired'
            outfile.write(outline + '\n')
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ' + DataDict[label]['PEbam'] + ' SAMstats-'
            outline = outline + label + '.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam ' + CCSnoM + ' /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
        
    outfile.close()

    print 'generating makewiggle.sh'
    outfile = open('makewiggle.sh','w')

    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        DataDict[label]['1x36mers.sacCer3.unique.nochrM.wig'] = label + '.1x36mers.sacCer3.unique.nochrM.wig'
        DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.wig'] = label + '.2x36mers.sacCer3.a.nochrM.ERMTOC.wig'
        DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig'] = label + '.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig'
        DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'] = label + '.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'
        DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp_sacCer.wig'] = label + '.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp_sacCer.wig'
        DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragment_sacCer.wig'] = label + '.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment_sacCer.wig'
        DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig'] = label + '.1x36mers.sacCer3.unique.nochrM.bigWig'
        DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig'] = label + '.2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig'
        DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.bigWig'] = label + '.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.bigWig'
        DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'] = label + '.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'
        DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp_sacCer.bigWig'] = label + '.2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp_sacCer.bigWig'
        DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragment_sacCer.bigWig'] = label + '.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment_sacCer.bigWig'
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['SEnochrMbam'] + ' ' + SCSnoM
        outline = outline + ' ' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.wig'] + ' -notitle -RPM'
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['PEbam'] + ' ' + SCSnoM
        outline = outline + ' ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.wig'] + ' -notitle -RPM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['PEbam'] + ' ' + SCSnoM
        outline = outline + ' ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig'] + ' -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment'
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['PEbam'] + ' ' + SCSnoM
        outline = outline + ' ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'] + ' -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25'
        outfile.write(outline + '\n')
        if species == 'S.pombe':
            DataDict[label]['1x36mers.spike.unique.nochrM.wig'] = label + '.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.wig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.wig'] = label + '.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.a.nochrM.ERMTOC.wig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragment.wig'] = label + '.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.a.nochrM.ERMTOC.fragment.wig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'] = label + '.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'
            DataDict[label]['1x36mers.spike.unique.nochrM.bigWig'] = label + '.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bigWig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig'] = label + '.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.a.nochrM.ERMTOC.bigWig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragment.bigWig'] = label + '.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.a.nochrM.ERMTOC.fragment.bigWig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'] = label + '.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['SEnochrMbam'] + ' ' + PCSnoM
            outline = outline + ' ' + DataDict[label]['1x36mers.spike.unique.nochrM.wig'] + ' -notitle -RPM'
            outfile.write(outline + '\n')
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['PEbam'] + ' ' + PCSnoM
            outline = outline + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.wig'] + ' -notitle -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['PEbam'] + ' ' + PCSnoM
            outline = outline + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragment.wig'] + ' -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment'
            outfile.write(outline + '\n')
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['PEbam'] + ' ' + PCSnoM
            outline = outline + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'] + ' -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25'
            outfile.write(outline + '\n')
        if species == 'Candida':
            DataDict[label]['1x36mers.spike.unique.nochrM.wig'] = label + '.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.wig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.wig'] = label + '.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.wig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragment.wig'] = label + '.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.wig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'] = label + '.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'
            DataDict[label]['1x36mers.spike.unique.nochrM.bigWig'] = label + '.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM.bigWig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig'] = label + '.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.bigWig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragment.bigWig'] = label + '.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragment.bigWig'
            DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'] = label + '.2x36mers.C_glabrata_CBS138_current_chromosomes.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['SEnochrMbam'] + ' ' + CCSnoM
            outline = outline + ' ' + DataDict[label]['1x36mers.spike.unique.nochrM.wig'] + ' -notitle -RPM'
            outfile.write(outline + '\n')
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['PEbam'] + ' ' + CCSnoM
            outline = outline + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.wig'] + ' -notitle -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['PEbam'] + ' ' + CCSnoM
            outline = outline + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragment.wig'] + ' -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragment'
            outfile.write(outline + '\n')
            outline = 'python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ' + DataDict[label]['PEbam'] + ' ' + CCSnoM
            outline = outline + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'] + ' -notitle -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint 25'
            outfile.write(outline + '\n')

    outfile.close()

    print 'generating columnrename.sh'
    outfile = open('columnrename.sh','w')

    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        print label
        print DataDict[label]
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/columnRename.py ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig']
        outline = outline + ' 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.old_to_new 1 0 > '
        outline = outline + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp_sacCer.wig']
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/columnRename.py ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig']
        outline = outline + ' 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.old_to_new 1 0 > '
        outline = outline + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragment_sacCer.wig']
        outfile.write(outline + '\n')

    outfile.close()

    print 'generating wigtobigwig.sh'
    outfile = open('wigtobigwig.sh','w')

    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.wig'] + ' ' + SCS + ' ' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig']
        outfile.write(outline + '\n')
        outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.wig'] + ' ' + SCS + ' ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig']
        outfile.write(outline + '\n')
        outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.wig'] + ' ' + SCS + ' ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragment.bigWig']
        outfile.write(outline + '\n')
        outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'] + ' ' + SCS + ' ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig']
        outfile.write(outline + '\n')
        outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp_sacCer.wig'] + ' ' + SC3CS + ' ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp_sacCer.bigWig']
        outfile.write(outline + '\n')
        outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragment_sacCer.wig'] + ' ' + SC3CS + ' ' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragment_sacCer.bigWig']
        outfile.write(outline + '\n')
        if species == 'S.pombe':
            outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['1x36mers.spike.unique.nochrM.wig'] + ' ' + PCS + ' ' + DataDict[label]['1x36mers.spike.unique.nochrM.bigWig']
            outfile.write(outline + '\n')
            outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.wig'] + ' ' + PCS + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig']
            outfile.write(outline + '\n')
            outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragment.wig'] + ' ' + PCS + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragment.bigWig']
            outfile.write(outline + '\n')
            outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'] + ' ' + PCS + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig']
            outfile.write(outline + '\n')
        if species == 'Candida':
            outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['1x36mers.spike.unique.nochrM.wig'] + ' ' + CCS + ' ' + DataDict[label]['1x36mers.spike.unique.nochrM.bigWig']
            outfile.write(outline + '\n')
            outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.wig'] + ' ' + CCS + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig']
            outfile.write(outline + '\n')
            outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragment.wig'] + ' ' + CCS + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragment.bigWig']
            outfile.write(outline + '\n')
            outline = '/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig'] + ' ' + CCS + ' ' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig']
            outfile.write(outline + '\n')

    outfile.close()

    print 'generating cumulativeGeneProfiles.sacCer3.files'
    outfile = open('cumulativeGeneProfiles.sacCer3.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.wig']
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating cumulativeGeneProfiles.Candida.files'
    outfile = open('cumulativeGeneProfiles.Candida.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + DataDict[label]['1x36mers.spike.unique.nochrM.wig']
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating cumulativeGeneProfiles.S_pombe.files'
    outfile = open('cumulativeGeneProfiles.S_pombe.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + DataDict[label]['1x36mers.spike.unique.nochrM.wig']
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating cumulativeGeneProfiles.with_multimappers.nochrM.ERMTOC.sacCer3.files'
    outfile = open('cumulativeGeneProfiles.with_multimappers.nochrM.ERMTOC.sacCer3.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.wig']
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating cumulativeGeneProfiles.with_multimappers.nochrM.ERMTOC.Candida.files'
    outfile = open('cumulativeGeneProfiles.with_multimappers.nochrM.ERMTOC.Candida.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.wig']
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating cumulativeGeneProfiles.with_multimappers.nochrM.ERMTOC.S_pombe.files'
    outfile = open('cumulativeGeneProfiles.with_multimappers.nochrM.ERMTOC.S_pombe.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.wig']
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating cumulativeGeneProfiles.with_multimappers.nochrM.ERMTOC.sacCer3-fullFragmentMidPoint.files'
    outfile = open('cumulativeGeneProfiles.with_multimappers.nochrM.ERMTOC.sacCer3-fullFragmentMidPoint.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.wig']
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAroundCoordinate.sh'
    outfile = open('signalAroundCoordinate.sh','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.tRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.tRNA.' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.snoRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.snoRNA.' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.snRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.snRNA.' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.rRNA.RDN5.genes 0 1 3 500 '
        outline = outline + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.rRNA.RDN5.' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig'][:-7]
        outfile.write(outline + '\n')

        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.tRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.tRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.snoRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.snoRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.snRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.snRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.rRNA.RDN5.genes 0 1 3 500 '
        outline = outline + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.rRNA.RDN5.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig'][:-7]
        outfile.write(outline + '\n')

        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.tRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.tRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.snoRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.snoRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.snRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.snRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.rRNA.RDN5.genes 0 1 3 500 '
        outline = outline + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig']
        outline = outline + ' signalAround-TSS.sacCer3.rRNA.RDN5.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'][:-7]
        outfile.write(outline + '\n')

        if species != 'S.pombe':
            continue
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.tRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['1x36mers.spike.unique.nochrM.bigWig']
        outline = outline + ' signalAround-TSS.S_pombe.tRNA.' + DataDict[label]['1x36mers.spike.unique.nochrM.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.snRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['1x36mers.spike.unique.nochrM.bigWig']
        outline = outline + ' signalAround-TSS.S_pombe.snRNA.' + DataDict[label]['1x36mers.spike.unique.nochrM.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.snoRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['1x36mers.spike.unique.nochrM.bigWig']
        outline = outline + ' signalAround-TSS.S_pombe.snoRNA.' + DataDict[label]['1x36mers.spike.unique.nochrM.bigWig'][:-7]
        outfile.write(outline + '\n')

        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.tRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig']
        outline = outline + ' signalAround-TSS.S_pombe.tRNA.' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.snRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig']
        outline = outline + ' signalAround-TSS.S_pombe.snRNA.' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig'][:-7]
        outfile.write(outline + '\n')
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.snoRNA.genes 0 1 3 500 '
        outline = outline + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig']
        outline = outline + ' signalAround-TSS.S_pombe.snoRNA.' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig'][:-7]
        outfile.write(outline + '\n')
        
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.unique.sacCer3.tRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.unique.sacCer3.tRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.tRNA.' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.unique.sacCer3.snoRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.unique.sacCer3.snoRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.snoRNA.' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.unique.sacCer3.snRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.unique.sacCer3.snRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.snRNA.' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.unique.sacCer3.rRNA.RDN5.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.unique.sacCer3.rRNA.RDN5.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.rRNA.RDN5.' + DataDict[label]['1x36mers.sacCer3.unique.nochrM.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.ERMTOC.sacCer3.tRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.ERMTOC.sacCer3.tRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.tRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.ERMTOC.sacCer3.snoRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.ERMTOC.sacCer3.snoRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.snoRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.ERMTOC.sacCer3.snRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.ERMTOC.sacCer3.snRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.snRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.ERMTOC.sacCer3.rRNA.RDN5.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.ERMTOC.sacCer3.rRNA.RDN5.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.rRNA.RDN5.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.tRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.tRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.tRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.snoRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.snoRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.snoRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.snRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.snRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.snRNA.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.rRNA.RDN5.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.rRNA.RDN5.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'signalAround-TSS.sacCer3.rRNA.RDN5.' + DataDict[label]['2x36mers.sacCer3.a.nochrM.ERMTOC.fragmentMidPoint_50bp.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.ERMTOC.S_pombe.tRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.ERMTOC.S_pombe.tRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'signalAround-TSS.S_pombe.tRNA.' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.ERMTOC.S_pombe.snRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.ERMTOC.S_pombe.snRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'signalAround-TSS.S_pombe.snRNA.' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating signalAround-TSS.with_multimappers.nochrM.ERMTOC.S_pombe.snoRNA.files'
    outfile = open('signalAround-TSS.with_multimappers.nochrM.ERMTOC.S_pombe.snoRNA.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'signalAround-TSS.S_pombe.snoRNA.' + DataDict[label]['2x36mers.spike.a.nochrM.ERMTOC.bigWig'][:-7] + '\t0\t1'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating bedRPKMfromBAM.sh'
    outfile = open('bedRPKMfromBAM.sh','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-upstream500bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-upstream500bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-250bp-350bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-250bp-350bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')

        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 '
        outline = outline + DataDict[label]['SEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-upstream500bp.sacCer3.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 '
        outline = outline + DataDict[label]['SEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-upstream500bp.sacCer3.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 '
        outline = outline + DataDict[label]['SEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-250bp-350bp.sacCer3.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 '
        outline = outline + DataDict[label]['SEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-250bp-350bp.sacCer3.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')

        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes_500bp_ext.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes_500bp_ext.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')

        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 '
        outline = outline + DataDict[label]['SEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes_500bp_ext.sacCer3.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 '
        outline = outline + DataDict[label]['SEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes_500bp_ext.sacCer3.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 '
        outline = outline + DataDict[label]['SEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes.sacCer3.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 '
        outline = outline + DataDict[label]['SEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes.sacCer3.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
        outfile.write(outline + '\n')

        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-upstream500bp.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-upstream500bp.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-250bp-350bp.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-250bp-350bp.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')

        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes_500bp_ext.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes_500bp_ext.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')

        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-upstream500bp.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-upstream500bp.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-250bp-350bp.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-250bp-350bp.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')

        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes_500bp_ext.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes_500bp_ext.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')

        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-upstream500bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-upstream500bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-250bp-350bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'TSS-250bp-350bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')

        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes_500bp_ext.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes_500bp_ext.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')
        outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 '
        outline = outline + DataDict[label]['PEbam'] + ' ' + SCSnoM + ' '
        outline = outline + 'genes.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
        outfile.write(outline + '\n')

        if species == 'S.pombe':
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes.S_pombe-spike-in.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes.S_pombe-spike-in.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes_500bp_ext.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes_500bp_ext.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + PCSnoM + ' '
            outline = outline + 'genes.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')

        if species == 'Candida':
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.Candida-spike-in.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.Candida-spike-in.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes_500bp_ext.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes_500bp_ext.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes_500bp_ext.Candida-spike-in.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes_500bp_ext.Candida-spike-in.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes.Candida-spike-in.' + label + '.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 '
            outline = outline + DataDict[label]['SEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes.Candida-spike-in.' + label + '.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes_500bp_ext.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes_500bp_ext.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-upstream500bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')

            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes_500bp_ext.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes_500bp_ext.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')
            outline = 'python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 '
            outline = outline + DataDict[label]['PEbam'] + ' ' + CCSnoM + ' '
            outline = outline + 'genes.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint'
            outfile.write(outline + '\n')

    outfile.close()

    print 'generating TSS-upstream500bp.sacCer3.RPM.files'
    outfile = open('TSS-upstream500bp.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-upstream500bp.sacCer3.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.sacCer3.RPKM.files'
    outfile = open('TSS-upstream500bp.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-upstream500bp.sacCer3.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.sacCer3.RPM.files'
    outfile = open('TSS-250bp-350bp.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-250bp-350bp.sacCer3.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.sacCer3.RPKM.files'
    outfile = open('TSS-250bp-350bp.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-250bp-350bp.sacCer3.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.sacCer3.RPM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-upstream500bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.sacCer3.RPKM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
	outline = label + '\t' + 'TSS-upstream500bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.sacCer3.RPM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-250bp-350bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.sacCer3.RPKM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-250bp-350bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.sacCer3.RPM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes_500bp_ext.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.sacCer3.RPKM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes_500bp_ext.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.sacCer3.RPM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.sacCer3.RPKM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.sacCer3.RPM.files'
    outfile = open('genes_500bp_ext.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes_500bp_ext.sacCer3.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.sacCer3.RPKM.files'
    outfile = open('genes_500bp_ext.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes_500bp_ext.sacCer3.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.sacCer3.RPM.files'
    outfile = open('genes.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes.sacCer3.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.sacCer3.RPKM.files'
    outfile = open('genes.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes.sacCer3.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-upstream500bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-upstream500bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-250bp-350bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-250bp-350bp.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes_500bp_ext.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes_500bp_ext.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-upstream500bp.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-upstream500bp.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-250bp-350bp.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-250bp-350bp.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('TSS-upstream500bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-upstream500bp.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('TSS-upstream500bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-upstream500bp.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('TSS-250bp-350bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-250bp-350bp.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('TSS-250bp-350bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'TSS-250bp-350bp.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes_500bp_ext.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes_500bp_ext.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('genes_500bp_ext.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes_500bp_ext.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('genes_500bp_ext.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes_500bp_ext.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files'
    outfile = open('genes.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files'
    outfile = open('genes.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.sacCer3.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        outline = label + '\t' + 'genes.protein_coding.merged.sacCer3.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.S_pombe.RPM.files'
    outfile = open('genes.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes.S_pombe-spike-in.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.S_pombe.RPKM.files'
    outfile = open('genes.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes.S_pombe-spike-in.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.S_pombe.RPM.files'
    outfile = open('genes_500bp_ext.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.S_pombe.RPKM.files'
    outfile = open('genes_500bp_ext.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.S_pombe.RPM.files'
    outfile = open('TSS-upstream500bp.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.S_pombe.RPKM.files'
    outfile = open('TSS-upstream500bp.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.S_pombe.RPM.files'
    outfile = open('TSS-250bp-350bp.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.S_pombe.RPKM.files'
    outfile = open('TSS-250bp-350bp.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.S_pombe.RPM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.S_pombe.RPKM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.S_pombe.RPM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.S_pombe.RPKM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.S_pombe.RPM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.S_pombe.RPKM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.S_pombe.RPM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.S_pombe.RPKM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes_500bp_ext.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes_500bp_ext.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes_500bp_ext.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('TSS-upstream500bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('TSS-upstream500bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('TSS-250bp-350bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('TSS-250bp-350bp.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('genes_500bp_ext.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('genes_500bp_ext.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files'
    outfile = open('genes.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files'
    outfile = open('genes.protein_coding.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.S_pombe.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'S.pombe':
            continue
        outline = label + '\t' + 'genes.protein_coding.merged.S_pombe-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.Candida.RPM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.Candida.RPKM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.Candida.RPM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.Candida.RPKM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.Candida.RPM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes_500bp_ext.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.Candida.RPKM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes_500bp_ext.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.Candida.RPM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.Candida.RPKM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.Candida.RPM.files'
    outfile = open('TSS-upstream500bp.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.Candida-spike-in.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.Candida.RPKM.files'
    outfile = open('TSS-upstream500bp.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.Candida-spike-in.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.Candida.RPM.files'
    outfile = open('TSS-250bp-350bp.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.Candida.RPKM.files'
    outfile = open('TSS-250bp-350bp.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.Candida.RPM.files'
    outfile = open('genes_500bp_ext.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes_500bp_ext.Candida-spike-in.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.Candida.RPKM.files'
    outfile = open('genes_500bp_ext.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes_500bp_ext.Candida-spike-in.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.Candida.RPM.files'
    outfile = open('genes.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes.Candida-spike-in.' + label + '.1x36mers.unique.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.Candida.RPKM.files'
    outfile = open('genes.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes.Candida-spike-in.' + label + '.1x36mers.unique.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files'
    outfile = open('TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files'
    outfile = open('TSS-upstream500bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files'
    outfile = open('TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files'
    outfile = open('TSS-250bp-350bp.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files'
    outfile = open('genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes_500bp_ext.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files'
    outfile = open('genes_500bp_ext.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes_500bp_ext.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files'
    outfile = open('genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files'
    outfile = open('genes.merged.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes.merged.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2\t3'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files'
    outfile = open('TSS-upstream500bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-upstream500bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files'
    outfile = open('TSS-250bp-350bp.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'TSS-250bp-350bp.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5,6\t7'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes_500bp_ext.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files'
    outfile = open('genes_500bp_ext.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes_500bp_ext.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

    print 'generating genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files'
    outfile = open('genes.with_multimappers.nochrM.ERMTOC.fragmentMidPoint.Candida.RPKM.files','w')
    for label in labels:
        (end1,end2,species) = DataDict[label]['input']
        if species != 'Candida':
            continue
        outline = label + '\t' + 'genes.Candida-spike-in.' + label + '.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM' + '\t0,1,2,3,4,5\t6'
        outfile.write(outline + '\n')
    outfile.close()

run()