galaxy/tools/samtools/sam_pileup.py

#!/usr/bin/env python

"""
Creates a pileup file from a bam file and a reference.

usage: %prog [options]
   -p, --input1=p: bam file
   -o, --output1=o: Output pileup
   -R, --ref=R: Reference file type
   -n, --ownFile=n: User-supplied fasta reference file
   -d, --dbkey=d: dbkey of user-supplied file
   -x, --indexDir=x: Index directory
   -b, --bamIndex=b: BAM index file
   -s, --lastCol=s: Print the mapping quality as the last column
   -i, --indels=i: Only output lines containing indels
   -M, --mapCap=M: Cap mapping quality
   -c, --consensus=c: Call the consensus sequence using MAQ consensu model
   -T, --theta=T: Theta paramter (error dependency coefficient)
   -N, --hapNum=N: Number of haplotypes in sample
   -r, --fraction=r: Expected fraction of differences between a pair of haplotypes
   -I, --phredProb=I: Phred probability of an indel in sequencing/prep

"""

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 )
    #prepare file names 
    tmpDir = tempfile.mkdtemp()
    tmpf0 = tempfile.NamedTemporaryFile( dir=tmpDir )
    tmpf0_name = tmpf0.name
    tmpf0.close()
    tmpf0bam_name = '%s.bam' % tmpf0_name
    tmpf0bambai_name = '%s.bam.bai' % tmpf0_name
    tmpf1 = tempfile.NamedTemporaryFile( dir=tmpDir )
    tmpf1_name = tmpf1.name
    tmpf1.close()
    tmpf1fai_name = '%s.fai' % tmpf1_name
    #link bam and bam index to working directory (can't move because need to leave original)
    os.symlink( options.input1, tmpf0bam_name )
    os.symlink( options.bamIndex, tmpf0bambai_name )
    #get parameters for pileup command
    if options.lastCol == 'yes':
        lastCol = '-s'
    else:
        lastCol = ''
    if options.indels == 'yes':
        indels = '-i'
    else:
        indels = ''
    opts = '%s %s -M %s' % ( lastCol, indels, options.mapCap )
    if options.consensus == 'yes':
        opts += ' -c -T %s -N %s -r %s -I %s' % ( options.theta, options.hapNum, options.fraction, options.phredProb )
    #prepare basic pileup command
    cmd = 'samtools pileup %s -f %s %s > %s'
    try:
        # have to nest try-except in try-finally to handle 2.4
        try:
            #index reference if necessary and prepare pileup command
            if options.ref == 'indexed':
                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 % ( opts, seqPath, tmpf0bam_name, options.output1 )
            elif options.ref == 'history':
                os.symlink( options.ownFile, tmpf1_name )
                cmdIndex = 'samtools faidx %s' % ( tmpf1_name )
                tmp = tempfile.NamedTemporaryFile( dir=tmpDir ).name
                tmp_stderr = open( tmp, 'wb' )
                proc = subprocess.Popen( args=cmdIndex, shell=True, cwd=tmpDir, stderr=tmp_stderr.fileno() )
                returncode = proc.wait()
                tmp_stderr.close()
                # 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()
                #did index succeed?
                if returncode != 0:
                    raise Exception, 'Error creating index file\n' + stderr
                cmd = cmd % ( opts, tmpf1_name, tmpf0bam_name, options.output1 )
            #perform pileup 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 Samtools pileup 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( 'Converted BAM to pileup' )
    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__()