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1 import sys
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2 import subprocess as sp
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3 import os
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4
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5 # Creates the sorted and indexed bam/bai files that are requried for both bam2wig and RSEQC_count
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6 def samtools_sorted(bam):
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7 sortedbam = bam + ".sorted"
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8 indexedbam = ".".join([sortedbam,"bam.bai"])
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9 sp.call(['samtools', 'sort', '-m 1000000000', bam, sortedbam])
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10 sortedbam = sortedbam + '.bam'
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11 sp.call(['samtools', 'index', sortedbam, indexedbam])
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12 return sortedbam
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13
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14 def main(args):
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15 args[2] = samtools_sorted(args[2])
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16 sp.call(args)
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17
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18
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19 if __name__ == "__main__":
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20 main(sys.argv[1:]) |
