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using samtools commands within python
Commands available in csamtools are available as simple function calls. For example:
pysam.sort( "ex1.bam", "output" )corresponds to the command line:
samtools sort ex1.bam output
Command line options can be provided as arguments:
pysam.sort( "-n", "ex1.bam", "output" )or:
pysam.sort( "-m", "1000000", "ex1.bam", "output" )In order to get usage information, try:
print pysam.sort.usage()Argument errors raise a pysam.SamtoolsError:
pysam.sort()Traceback (most recent call last):File "x.py", line 12, in <module> pysam.sort()File "/home/andreas/pysam/build/lib.linux-x86_64-2.6/pysam/__init__.py", line 37, in __call__ if retval: raise SamtoolsError( "\n".join( stderr ) )pysam.SamtoolsError: ‘Usage: samtools sort [-n] [-m <maxMem>] <in.bam> <out.prefix>\n‘
Messages from csamtools on stderr are captured and are available using the getMessages() method:
pysam.sort.getMessage()Note that only the output from the last invocation of a command is stored.
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