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345 lines
18 KiB
Python
345 lines
18 KiB
Python
#!/usr/bin/env python
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"""
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Runs BFAST on single-end or paired-end data.
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TODO: more documentation
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TODO:
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- auto-detect gzip or bz2
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- split options (?)
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- queue lengths (?)
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- assumes reference always has been indexed
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- main and secondary indexes
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- scoring matrix file ?
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- read group file ?
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usage: bfast_wrapper.py [options]
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-r, --ref=r: The reference genome to use or index
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-f, --fastq=f: The fastq file to use for the mapping
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-F, --output=u: The file to save the output (SAM format)
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-s, --fileSource=s: Whether to use a previously indexed reference sequence or one from history (indexed or history)
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-p, --params=p: Parameter setting to use (pre_set or full)
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-n, --numThreads=n: The number of threads to use
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-A, --space=A: The encoding space (0: base 1: color)
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-o, --offsets=o: The offsets for 'match'
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-l, --loadAllIndexes=l: Load all indexes into memory
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-k, --keySize=k: truncate key size in 'match'
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-K, --maxKeyMatches=K: the maximum number of matches to allow before a key is ignored
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-M, --maxNumMatches=M: the maximum number of matches to allow before the read is discarded
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-w, --whichStrand=w: the strands to consider (0: both 1: forward 2: reverse)
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-t, --timing=t: output timing information to stderr
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-u, --ungapped=u: performed ungapped local alignment
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-U, --unconstrained=U: performed local alignment without mask constraints
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-O, --offset=O: the number of bases before and after each hit to consider in local alignment
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-q, --avgMismatchQuality=q: average mismatch quality
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-a, --algorithm=a: post processing algorithm (0: no filtering, 1: all passing filters, 2: unique, 3: best scoring unique, 4: best score all)
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-P, --disallowPairing=P: do not choose alignments based on pairing
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-R, --reverse=R: paired end reads are given on reverse strands
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-z, --random=z: output a random best scoring alignment
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-D, --dbkey=D: Dbkey for reference genome
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-H, --suppressHeader=H: Suppress the sam header
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"""
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import optparse, os, shutil, subprocess, sys, tempfile
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def stop_err( msg ):
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sys.stderr.write( '%s\n' % msg )
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sys.exit()
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def __main__():
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#Parse Command Line
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parser = optparse.OptionParser()
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parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to index and use' )
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parser.add_option( '-f', '--fastq', dest='fastq', help='The fastq file to use for the mapping' )
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parser.add_option( '-F', '--output', dest='output', help='The file to save the output (SAM format)' )
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parser.add_option( '-A', '--space', dest='space', type="choice", default='0', choices=('0','1' ), help='The encoding space (0: base 1: color)' )
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parser.add_option( '-H', '--suppressHeader', action="store_true", dest='suppressHeader', default=False, help='Suppress header' )
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parser.add_option( '-n', '--numThreads', dest='numThreads', type="int", default="1", help='The number of threads to use' )
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parser.add_option( '-t', '--timing', action="store_true", default=False, dest='timing', help='output timming information to stderr' )
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parser.add_option( '-l', '--loadAllIndexes', action="store_true", default=False, dest='loadAllIndexes', help='Load all indexes into memory' )
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parser.add_option( '-m', '--indexMask', dest='indexMask', help='String containing info on how to build custom indexes' )
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parser.add_option( "-b", "--buildIndex", action="store_true", dest="buildIndex", default=False, help='String containing info on how to build custom indexes' )
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parser.add_option( "--indexRepeatMasker", action="store_true", dest="indexRepeatMasker", default=False, help='Do not index lower case sequences. Such as those created by RepeatMasker' )
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parser.add_option( '--indexContigOptions', dest='indexContigOptions', default="", help='The contig range options to use for the indexing' )
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parser.add_option( '--indexExonsFileName', dest='indexExonsFileName', default="", help='The exons file to use for the indexing' )
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parser.add_option( '-o', '--offsets', dest='offsets', default="", help='The offsets for \'match\'' )
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parser.add_option( '-k', '--keySize', dest='keySize', type="int", default="-1", help='truncate key size in \'match\'' )
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parser.add_option( '-K', '--maxKeyMatches', dest='maxKeyMatches', type="int", default="-1", help='the maximum number of matches to allow before a key is ignored' )
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parser.add_option( '-M', '--maxNumMatches', dest='maxNumMatches', type="int", default="-1", help='the maximum number of matches to allow bfore the read is discarded' )
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parser.add_option( '-w', '--whichStrand', dest='whichStrand', type="choice", default='0', choices=('0','1','2'), help='the strands to consider (0: both 1: forward 2: reverse)' )
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parser.add_option( '--scoringMatrixFileName', dest='scoringMatrixFileName', help='Scoring Matrix file used to score the alignments' )
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parser.add_option( '-u', '--ungapped', dest='ungapped', action="store_true", default=False, help='performed ungapped local alignment' )
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parser.add_option( '-U', '--unconstrained', dest='unconstrained', action="store_true", default=False, help='performed local alignment without mask constraints' )
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parser.add_option( '-O', '--offset', dest='offset', type="int", default="0", help='the number of bases before and after each hit to consider in local alignment' )
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parser.add_option( '-q', '--avgMismatchQuality', type="int", default="-1", dest='avgMismatchQuality', help='average mismatch quality' )
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parser.add_option( '-a', '--algorithm', dest='algorithm', default='0', type="choice", choices=('0','1','2','3','4' ), help='post processing algorithm (0: no filtering, 1: all passing filters, 2: unique, 3: best scoring unique, 4: best score all' )
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parser.add_option( '--unpaired', dest='unpaired', action="store_true", default=False, help='do not choose alignments based on pairing' )
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parser.add_option( '--reverseStrand', dest='reverseStrand', action="store_true", default=False, help='paired end reads are given on reverse strands' )
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parser.add_option( '--pairedEndInfer', dest='pairedEndInfer', action="store_true", default=False, help='break ties when one end of a paired end read by estimating the insert size distribution' )
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parser.add_option( '--randomBest', dest='randomBest', action="store_true", default=False, help='output a random best scoring alignment' )
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(options, args) = parser.parse_args()
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# output version # of tool
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try:
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tmp = tempfile.NamedTemporaryFile().name
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tmp_stdout = open( tmp, 'wb' )
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proc = subprocess.Popen( args='bfast 2>&1', shell=True, stdout=tmp_stdout )
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tmp_stdout.close()
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returncode = proc.wait()
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stdout = None
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for line in open( tmp_stdout.name, 'rb' ):
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if line.lower().find( 'version' ) >= 0:
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stdout = line.strip()
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break
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if stdout:
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sys.stdout.write( '%s\n' % stdout )
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else:
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raise Exception
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except:
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sys.stdout.write( 'Could not determine BFAST version\n' )
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buffsize = 1048576
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# make temp directory for bfast, requires trailing slash
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tmp_dir = '%s/' % tempfile.mkdtemp()
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#'generic' options used in all bfast commands here
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if options.timing:
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all_cmd_options = "-t"
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else:
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all_cmd_options = ""
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try:
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if options.buildIndex:
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reference_filepath = tempfile.NamedTemporaryFile( dir=tmp_dir, suffix='.fa' ).name
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#build bfast indexes
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os.symlink( options.ref, reference_filepath )
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#bfast fast2brg
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try:
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nuc_space = [ "0" ]
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if options.space == "1":
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#color space localalign appears to require nuc space brg
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nuc_space.append( "1" )
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for space in nuc_space:
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cmd = 'bfast fasta2brg -f "%s" -A "%s" %s' % ( reference_filepath, space, all_cmd_options )
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tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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tmp_stderr = open( tmp, 'wb' )
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proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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returncode = proc.wait()
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tmp_stderr.close()
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# get stderr, allowing for case where it's very large
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tmp_stderr = open( tmp, 'rb' )
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stderr = ''
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try:
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while True:
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stderr += tmp_stderr.read( buffsize )
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if not stderr or len( stderr ) % buffsize != 0:
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break
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except OverflowError:
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pass
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tmp_stderr.close()
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if returncode != 0:
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raise Exception, stderr
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except Exception, e:
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raise Exception, 'Error in \'bfast fasta2brg\'.\n' + str( e )
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#bfast index
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try:
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all_index_cmds = 'bfast index %s -f "%s" -A "%s" -n "%s"' % ( all_cmd_options, reference_filepath, options.space, options.numThreads )
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if options.indexRepeatMasker:
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all_index_cmds += " -R"
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if options.indexContigOptions:
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index_contig_options = map( int, options.indexContigOptions.split( ',' ) )
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if index_contig_options[0] >= 0:
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all_index_cmds += ' -s "%s"' % index_contig_options[0]
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if index_contig_options[1] >= 0:
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all_index_cmds += ' -S "%s"' % index_contig_options[1]
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if index_contig_options[2] >= 0:
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all_index_cmds += ' -e "%s"' % index_contig_options[2]
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if index_contig_options[3] >= 0:
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all_index_cmds += ' -E "%s"' % index_contig_options[3]
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elif options.indexExonsFileName:
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all_index_cmds += ' -x "%s"' % options.indexExonsFileName
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index_count = 1
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for mask, hash_width in [ mask.split( ':' ) for mask in options.indexMask.split( ',' ) ]:
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cmd = '%s -m "%s" -w "%s" -i "%i"' % ( all_index_cmds, mask, hash_width, index_count )
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tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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tmp_stderr = open( tmp, 'wb' )
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proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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returncode = proc.wait()
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tmp_stderr.close()
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# get stderr, allowing for case where it's very large
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tmp_stderr = open( tmp, 'rb' )
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stderr = ''
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try:
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while True:
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stderr += tmp_stderr.read( buffsize )
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if not stderr or len( stderr ) % buffsize != 0:
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break
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except OverflowError:
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pass
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tmp_stderr.close()
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if returncode != 0:
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raise Exception, stderr
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index_count += 1
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except Exception, e:
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raise Exception, 'Error in \'bfast index\'.\n' + str( e )
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else:
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reference_filepath = options.ref
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assert reference_filepath and os.path.exists( reference_filepath ), 'A valid genome reference was not provided.'
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# set up aligning and generate aligning command options
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# set up temp output files
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tmp_bmf = tempfile.NamedTemporaryFile( dir=tmp_dir )
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tmp_bmf_name = tmp_bmf.name
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tmp_bmf.close()
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tmp_baf = tempfile.NamedTemporaryFile( dir=tmp_dir )
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tmp_baf_name = tmp_baf.name
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tmp_baf.close()
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bfast_match_cmd = 'bfast match -f "%s" -r "%s" -n "%s" -A "%s" -T "%s" -w "%s" %s' % ( reference_filepath, options.fastq, options.numThreads, options.space, tmp_dir, options.whichStrand, all_cmd_options )
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bfast_localalign_cmd = 'bfast localalign -f "%s" -m "%s" -n "%s" -A "%s" -o "%s" %s' % ( reference_filepath, tmp_bmf_name, options.numThreads, options.space, options.offset, all_cmd_options )
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bfast_postprocess_cmd = 'bfast postprocess -O 1 -f "%s" -i "%s" -n "%s" -A "%s" -a "%s" %s' % ( reference_filepath, tmp_baf_name, options.numThreads, options.space, options.algorithm, all_cmd_options )
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if options.offsets:
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bfast_match_cmd += ' -o "%s"' % options.offsets
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if options.keySize >= 0:
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bfast_match_cmd += ' -k "%s"' % options.keySize
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if options.maxKeyMatches >= 0:
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bfast_match_cmd += ' -K "%s"' % options.maxKeyMatches
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if options.maxNumMatches >= 0:
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bfast_match_cmd += ' -M "%s"' % options.maxNumMatches
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bfast_localalign_cmd += ' -M "%s"' % options.maxNumMatches
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if options.scoringMatrixFileName:
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bfast_localalign_cmd += ' -x "%s"' % options.scoringMatrixFileName
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bfast_postprocess_cmd += ' -x "%s"' % options.scoringMatrixFileName
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if options.ungapped:
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bfast_localalign_cmd += ' -u'
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if options.unconstrained:
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bfast_localalign_cmd += ' -U'
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if options.avgMismatchQuality >= 0:
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bfast_localalign_cmd += ' -q "%s"' % options.avgMismatchQuality
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bfast_postprocess_cmd += ' -q "%s"' % options.avgMismatchQuality
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if options.algorithm == 3:
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if options.pairedEndInfer:
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bfast_postprocess_cmd += ' -P'
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if options.randomBest:
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bfast_postprocess_cmd += ' -z'
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if options.unpaired:
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bfast_postprocess_cmd += ' -U'
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if options.reverseStrand:
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bfast_postprocess_cmd += ' -R'
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#instead of using temp files, should we stream through pipes?
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bfast_match_cmd += " > %s" % tmp_bmf_name
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bfast_localalign_cmd += " > %s" % tmp_baf_name
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bfast_postprocess_cmd += " > %s" % options.output
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# need to nest try-except in try-finally to handle 2.4
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try:
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# bfast 'match'
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try:
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tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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tmp_stderr = open( tmp, 'wb' )
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proc = subprocess.Popen( args=bfast_match_cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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returncode = proc.wait()
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tmp_stderr.close()
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# get stderr, allowing for case where it's very large
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tmp_stderr = open( tmp, 'rb' )
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stderr = ''
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try:
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while True:
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stderr += tmp_stderr.read( buffsize )
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if not stderr or len( stderr ) % buffsize != 0:
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break
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except OverflowError:
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pass
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tmp_stderr.close()
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if returncode != 0:
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raise Exception, stderr
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except Exception, e:
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raise Exception, 'Error in \'bfast match\'. \n' + str( e )
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# bfast 'localalign'
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try:
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tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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tmp_stderr = open( tmp, 'wb' )
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proc = subprocess.Popen( args=bfast_localalign_cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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returncode = proc.wait()
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tmp_stderr.close()
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# get stderr, allowing for case where it's very large
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tmp_stderr = open( tmp, 'rb' )
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stderr = ''
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try:
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while True:
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stderr += tmp_stderr.read( buffsize )
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if not stderr or len( stderr ) % buffsize != 0:
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break
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except OverflowError:
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pass
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tmp_stderr.close()
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if returncode != 0:
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raise Exception, stderr
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except Exception, e:
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raise Exception, 'Error in \'bfast localalign\'. \n' + str( e )
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# bfast 'postprocess'
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try:
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tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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tmp_stderr = open( tmp, 'wb' )
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proc = subprocess.Popen( args=bfast_postprocess_cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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returncode = proc.wait()
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tmp_stderr.close()
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# get stderr, allowing for case where it's very large
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tmp_stderr = open( tmp, 'rb' )
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stderr = ''
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try:
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while True:
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stderr += tmp_stderr.read( buffsize )
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if not stderr or len( stderr ) % buffsize != 0:
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break
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except OverflowError:
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pass
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tmp_stderr.close()
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if returncode != 0:
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raise Exception, stderr
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except Exception, e:
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raise Exception, 'Error in \'bfast postprocess\'. \n' + str( e )
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# remove header if necessary
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if options.suppressHeader:
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tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
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tmp_out_name = tmp_out.name
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tmp_out.close()
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try:
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shutil.move( options.output, tmp_out_name )
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except Exception, e:
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raise Exception, 'Error moving output file before removing headers. \n' + str( e )
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fout = file( options.output, 'w' )
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for line in file( tmp_out.name, 'r' ):
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if len( line ) < 3 or line[0:3] not in [ '@HD', '@SQ', '@RG', '@PG', '@CO' ]:
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fout.write( line )
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fout.close()
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# check that there are results in the output file
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if os.path.getsize( options.output ) > 0:
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if "0" == options.space:
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sys.stdout.write( 'BFAST run on Base Space data' )
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else:
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sys.stdout.write( 'BFAST run on Color Space data' )
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else:
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raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.'
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except Exception, e:
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stop_err( 'The alignment failed.\n' + str( e ) )
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finally:
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# clean up temp dir
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if os.path.exists( tmp_dir ):
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shutil.rmtree( tmp_dir )
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if __name__=="__main__": __main__()
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