annotate SNV/snvmix.py @ 5:a4975ec34575

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#!/usr/bin/env python

"""
Runs the SNVMix2 binary on a bam input file with various options.

usage: %prog [options]
   -i, --input1=i: bam file
   -o, --output1=o: Output SNVMix (raw)
   -d, --dbkey=d: dbkey of user-supplied file
   -x, --indexDir=x: index directory
   -t, --type=t: analysis type (e.g. mb|m|b|M|Mb|MB|SNVMix1)
   -q, --base=q: base qual threshold
   -Q, --map=Q: map qual threshold
   -l, --pos=l: position file
   -f, --full=f: Full mode (output scores for every position)
   -R, --keep_dups: Retain reads flagged as duplicates (not recommended!)
   -c, --keep_chastity: Retain reads that failed the chastity filter
"""

import os, shutil, subprocess, sys, tempfile
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.cookbook import doc_optparse



def stop_err( msg ):
    sys.stderr.write( '%s\n' % msg )
    sys.exit()

def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ):
    seqFile = '%s/sam_fa_indices.loc' % GALAXY_DATA_INDEX_DIR
    seqPath = ''
    for line in open( seqFile ):
        line = line.rstrip( '\r\n' )
        if line and not line.startswith( '#' ) and line.startswith( 'index' ):
            fields = line.split( '\t' )
            if len( fields ) < 3:
                continue
            if fields[1] == dbkey:
                seqPath = fields[2].strip()
                break
    return seqPath

def __main__():
    #Parse Command Line
    options, args = doc_optparse.parse( __doc__ )
    seqPath = check_seq_file( options.dbkey, options.indexDir )

    #make temp dir
    tmpDir = tempfile.mkdtemp()
    
    #prepare basic SNVMix2 command
    cmd = 'SNVMix2 -p b -i %s -r %s -o %s -q %s -Q %s -t %s'
    try:
        # have to nest try-except in try-finally to handle 2.4
        try:
            if not os.path.exists( "%s.fai" % seqPath ):
                raise Exception, "No sequences are available for '%s', request them by reporting this error." % options.dbkey
            cmd = cmd % ( options.input1, seqPath, options.output1, options.base, options.map, options.type)
            
            if options.pos != "none":
                if os.path.isfile(options.pos):
                    cmd = cmd + ' -l ' + options.pos
                    if options.full == "yes":
                        cmd = cmd + ' -f '
                else:
                    raise Exception, "position file doesn't exist"

            if options.keep_chastity == "yes":
                cmd = cmd + ' -c'
            if options.keep_dups == "yes":
                cmd = cmd + ' -R'

            #perform SNVMix2 command
            tmp = tempfile.NamedTemporaryFile( dir=tmpDir ).name
            tmp_stderr = open( tmp, 'wb' )

            proc = subprocess.Popen( args=cmd, shell=True, cwd=tmpDir, stderr=tmp_stderr.fileno() )
            returncode = proc.wait()
            tmp_stderr.close()
            #did it succeed?
            # get stderr, allowing for case where it's very large
            tmp_stderr = open( tmp, 'rb' )
            stderr = ''
            buffsize = 1048576
            try:
                while True:
                    stderr += tmp_stderr.read( buffsize )
                    if not stderr or len( stderr ) % buffsize != 0:
                        break
            except OverflowError:
                pass
            tmp_stderr.close()
            if returncode != 0:
                raise Exception, stderr
        except Exception, e:
            stop_err( 'Error running SNVMix2 tool\n' + str( e ) )
    finally:
        #clean up temp files
        if os.path.exists( tmpDir ):
            shutil.rmtree( tmpDir )
    # check that there are results in the output file
    if os.path.getsize( options.output1 ) > 0:
        sys.stdout.write( 'wrote SNVMix output' )
    else:
        stop_err( 'The output file is empty. Your input file may have had no matches, or there may be an error with your input file or settings.' )

if __name__ == "__main__" : __main__()