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Several small changes to Samtools pileup tool to get it to work with user-supplied reference genome

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This commit is contained in:
Kelly Vincent
2009-10-05 10:35:39 -04:00
parent b83b40125b
commit 0ffbe38fc3
1 changed files with 6 additions and 4 deletions
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tools/samtools/sam_pileup.py
+6 -4
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@@ -68,14 +68,16 @@ def __main__():
stop_err( "No sequences are available for '%s', request them by reporting this error." % options.dbkey )
cmd3 = cmd3 % (opts, seq_path, tmpf0bam, options.output1)
elif options.ref == 'history':
cmd1 = 'cp %s %s; cp %s.fai %s' % (options.ownFile, tmpf1.name, options.ownFile, tmpf1fai)
cmd1 = 'cp %s %s; samtools faidx %s' % (options.ownFile, tmpf1.name, tmpf1.name)
cmd3 = cmd3 % (opts, tmpf1.name, tmpf0bam, options.output1)
# index reference if necessary
if cmd1:
try:
os.system(cmd1)
if options.ref == 'history' and not os.path.exists( tmpf1fai ):
stop_err( "Problem creating index file from history item." )
except Exception, eq:
stop_err('Error moving reference sequence\n' + str(eq))
stop_err('Error handling reference sequence\n' + str(eq))
# copy bam index to working directory
try:
os.system(cmd2)
@@ -85,7 +87,7 @@ def __main__():
try:
os.system(cmd3)
except Exception, eq:
stop_err('Error running SAMtools merge tool\n' + str(eq))
stop_err('Error running SAMtools pileup tool\n' + str(eq))
# clean up temp files
tmpf1.close()
tmpf0.close()
@@ -94,6 +96,6 @@ def __main__():
if os.path.exists(tmpf0bambai):
os.remove(tmpf0bambai)
if os.path.exists(tmpf1fai):
os.remove(tmpf0bambai)
os.remove(tmpf1fai)
if __name__ == "__main__" : __main__()