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#                                #
# Last modified 2023/07/25       # 
#                                #
# Georgi Marinov                 #
#                                # 
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import sys
import string
import numpy
from sets import Set

def run():

    if len(sys.argv) < 2:
        print 'usage: python %s config outfile' % sys.argv[0]
        print '\tconfig format:'
        print '\t\tlabel\tlist1,list2,list3,....,listN'
        sys.exit(1)

    outfile = open(sys.argv[2], 'w')

    lineslist = open(sys.argv[1])
    for line in lineslist:
        fields = line.strip().split('\t')
        label = fields[0]
        files = fields[1].split(',')
        Flist = []
        for file in files:
            lines = open(file)
            for L in lines:
                Flist.append(L.strip())
        outline = 'samtools merge -f ' + label + '.merged.bam'
        for F in Flist:
            outline = outline + ' ' + F
        outfile.write(outline + '\n')

    outfile.close()

run()