##################################
#                                #
# Last modified 2025/05/25       # 
#                                #
# Georgi Marinov                 #
#                                # 
##################################

import sys
import os
import random
import string

def run():

    if len(sys.argv) < 2:
        print 'usage: python %s input output' % sys.argv[0]
        sys.exit(1)

    input = sys.argv[1]
    output = sys.argv[2]

    outfile = open(output, 'w')

    cmd = 'cat ' + input
    p = os.popen(cmd, "r")
    line = 'line'
    while line != '':
        line = p.readline().strip()
        if line == '':
            break
        outline = 'python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa '
        outline += line.strip()
        outline += ' 0 1 2 50 '
        outline += line.strip()
        outline += '.NMI'
        outfile.write(outline + '\n')

run()