| Previous changeset 1:d9ac0d9cb48e (2013-07-08) Next changeset 3:203bda4cf122 (2013-07-08) |
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Commit message:
Uploaded |
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added:
samtoolshelper.py |
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| diff -r d9ac0d9cb48e -r 4d701c67592a samtoolshelper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtoolshelper.py Mon Jul 08 22:03:50 2013 -0400 |
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| @@ -0,0 +1,20 @@ +import sys +import subprocess as sp +import os + +# Creates the sorted and indexed bam/bai files that are requried for both bam2wig and RSEQC_count +def samtools_sorted(bam): + sortedbam = bam + ".sorted" + indexedbam = ".".join([sortedbam,"bam.bai"]) + sp.call(['samtools', 'sort', '-m 1000000000', bam, sortedbam]) + sortedbam = sortedbam + '.bam' + sp.call(['samtools', 'index', sortedbam, indexedbam]) + return sortedbam + +def main(args): + args[2] = samtools_sorted(args[2]) + sp.call(args) + + +if __name__ == "__main__": + main(sys.argv[1:]) \ No newline at end of file |