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470 lines
28 KiB
Python
470 lines
28 KiB
Python
#!/usr/bin/env python
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"""
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Runs Bowtie on single-end or paired-end data.
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For use with Bowtie v. 0.12.7
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usage: bowtie_wrapper.py [options]
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-t, --threads=t: The number of threads to run
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-o, --output=o: The output file
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--output_unmapped_reads=: File name for unmapped reads (single-end)
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--output_unmapped_reads_l=: File name for unmapped reads (left, paired-end)
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--output_unmapped_reads_r=: File name for unmapped reads (right, paired-end)
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--output_suppressed_reads=: File name for suppressed reads because of max setting (single-end)
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--output_suppressed_reads_l=: File name for suppressed reads because of max setting (left, paired-end)
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--output_suppressed_reads_r=: File name for suppressed reads because of max setting (right, paired-end)
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-i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format
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-I, --input2=I: The reverse reads file in Sanger FASTQ format
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-4, --dataType=4: The type of data (SOLiD or Solexa)
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-2, --paired=2: Whether the data is single- or paired-end
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-g, --genomeSource=g: The type of reference provided
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-r, --ref=r: The reference genome to use or index
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-s, --skip=s: Skip the first n reads
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-a, --alignLimit=a: Only align the first n reads
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-T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment
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-L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment
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-m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed
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-M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions
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-l, --seedLen=l: Seed length
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-n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30
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-P, --maqSoapAlign=P: Choose MAQ- or SOAP-like alignment policy
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-w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist
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-v, --valAlign=v: Report up to n valid arguments per read
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-V, --allValAligns=V: Whether or not to report all valid alignments per read
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-G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist
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-b, --best=b: Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions
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-B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read
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-R, --strata=R: Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable
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-j, --minInsert=j: Minimum insert size for valid paired-end alignments
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-J, --maxInsert=J: Maximum insert size for valid paired-end alignments
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-O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand
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-A, --maxAlignAttempt=A: Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate
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-f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand
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-E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand
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-F, --offrate=F: Override the offrate of the index to n
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-8, --snpphred=8: SNP penalty on Phred scale
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-6, --snpfrac=6: Fraction of sites expected to be SNP sites
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-7, --keepends=7: Keep extreme-end nucleotides and qualities
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-S, --seed=S: Seed for pseudo-random number generator
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-C, --params=C: Whether to use default or specified parameters
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-u, --iautoB=u: Automatic or specified behavior
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-K, --ipacked=K: Whether or not to use a packed representation for DNA strings
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-Q, --ibmax=Q: Maximum number of suffixes allowed in a block
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-Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference
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-D, --idcv=D: The period for the difference-cover sample
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-U, --inodc=U: Whether or not to disable the use of the difference-cover sample
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-y, --inoref=y: Whether or not to build the part of the reference index used only in paired-end alignment
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-z, --ioffrate=z: How many rows get marked during annotation of some or all of the Burrows-Wheeler rows
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-W, --iftab=W: The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query
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-X, --intoa=X: Whether or not to convert Ns in the reference sequence to As
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-N, --iendian=N: Endianness to use when serializing integers to the index file
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-Z, --iseed=Z: Seed for the pseudorandom number generator
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-c, --icutoff=c: Number of first bases of the reference sequence to index
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-x, --indexSettings=x: Whether or not indexing options are to be set
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-H, --suppressHeader=H: Suppress header
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--do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
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"""
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import optparse, os, shutil, subprocess, sys, tempfile
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#Allow more than Sanger encoded variants
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DEFAULT_ASCII_ENCODING = '--phred33-quals'
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GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = { 'fastqsanger':'--phred33-quals', 'fastqillumina':'--phred64-quals', 'fastqsolexa':'--solexa-quals' }
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#FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config
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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( '-t', '--threads', dest='threads', help='The number of threads to run' )
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parser.add_option( '-o', '--output', dest='output', help='The output file' )
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parser.add_option( '', '--output_unmapped_reads', dest='output_unmapped_reads', help='File name for unmapped reads (single-end)' )
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parser.add_option( '', '--output_unmapped_reads_l', dest='output_unmapped_reads_l', help='File name for unmapped reads (left, paired-end)' )
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parser.add_option( '', '--output_unmapped_reads_r', dest='output_unmapped_reads_r', help='File name for unmapped reads (right, paired-end)' )
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parser.add_option( '', '--output_suppressed_reads', dest='output_suppressed_reads', help='File name for suppressed reads because of max setting (single-end)' )
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parser.add_option( '', '--output_suppressed_reads_l', dest='output_suppressed_reads_l', help='File name for suppressed reads because of max setting (left, paired-end)' )
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parser.add_option( '', '--output_suppressed_reads_r', dest='output_suppressed_reads_r', help='File name for suppressed reads because of max setting (right, paired-end)' )
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parser.add_option( '-4', '--dataType', dest='dataType', help='The type of data (SOLiD or Solexa)' )
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parser.add_option( '-i', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
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parser.add_option( '-I', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
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parser.add_option( '-2', '--paired', dest='paired', help='Whether the data is single- or paired-end' )
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parser.add_option( '-g', '--genomeSource', dest='genomeSource', help='The type of reference provided' )
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parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' )
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parser.add_option( '-s', '--skip', dest='skip', help='Skip the first n reads' )
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parser.add_option( '-a', '--alignLimit', dest='alignLimit', help='Only align the first n reads' )
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parser.add_option( '-T', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment' )
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parser.add_option( '-L', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment' )
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parser.add_option( '-m', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed' )
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parser.add_option( '-M', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions' )
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parser.add_option( '-l', '--seedLen', dest='seedLen', help='Seed length' )
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parser.add_option( '-n', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30' )
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parser.add_option( '-P', '--maqSoapAlign', dest='maqSoapAlign', help='Choose MAQ- or SOAP-like alignment policy' )
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parser.add_option( '-w', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist' )
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parser.add_option( '-v', '--valAlign', dest='valAlign', help='Report up to n valid arguments per read' )
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parser.add_option( '-V', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read' )
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parser.add_option( '-G', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist' )
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parser.add_option( '-b', '--best', dest='best', help="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions" )
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parser.add_option( '-B', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read' )
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parser.add_option( '-R', '--strata', dest='strata', help='Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable' )
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parser.add_option( '-j', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments' )
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parser.add_option( '-J', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments' )
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parser.add_option( '-O', '--mateOrient', dest='mateOrient', help='The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand' )
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parser.add_option( '-A', '--maxAlignAttempt', dest='maxAlignAttempt', help='Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate' )
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parser.add_option( '-f', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand' )
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parser.add_option( '-E', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand' )
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parser.add_option( '-F', '--offrate', dest='offrate', help='Override the offrate of the index to n' )
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parser.add_option( '-S', '--seed', dest='seed', help='Seed for pseudo-random number generator' )
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parser.add_option( '-8', '--snpphred', dest='snpphred', help='SNP penalty on Phred scale' )
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parser.add_option( '-6', '--snpfrac', dest='snpfrac', help='Fraction of sites expected to be SNP sites' )
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parser.add_option( '-7', '--keepends', dest='keepends', help='Keep extreme-end nucleotides and qualities' )
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parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' )
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parser.add_option( '-u', '--iautoB', dest='iautoB', help='Automatic or specified behavior' )
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parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' )
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parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' )
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parser.add_option( '-Y', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference' )
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parser.add_option( '-D', '--idcv', dest='idcv', help='The period for the difference-cover sample' )
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parser.add_option( '-U', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample' )
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parser.add_option( '-y', '--inoref', dest='inoref', help='Whether or not to build the part of the reference index used only in paired-end alignment' )
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parser.add_option( '-z', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows' )
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parser.add_option( '-W', '--iftab', dest='iftab', help='The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query' )
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parser.add_option( '-X', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As' )
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parser.add_option( '-N', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file' )
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parser.add_option( '-Z', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator' )
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parser.add_option( '-c', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index' )
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parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' )
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parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
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parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fastqsanger", help='galaxy input format' )
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parser.add_option( '--do_not_build_index', dest='do_not_build_index', action="store_true", default=False, help='Flag to specify that provided file is already indexed, use as is' )
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(options, args) = parser.parse_args()
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stdout = ''
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# make temp directory for placement of indices and copy reference file there if necessary
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tmp_index_dir = tempfile.mkdtemp()
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# get type of data (solid or solexa)
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if options.dataType == 'solid':
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colorspace = '-C'
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else:
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colorspace = ''
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# index if necessary
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if options.genomeSource == 'history' and not options.do_not_build_index:
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# set up commands
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if options.index_settings =='indexPreSet':
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indexing_cmds = '%s' % colorspace
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else:
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try:
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if options.iautoB and options.iautoB == 'set':
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iautoB = '--noauto'
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else:
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iautoB = ''
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if options. ipacked and options.ipacked == 'packed':
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ipacked = '--packed'
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else:
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ipacked = ''
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if options.ibmax and int( options.ibmax ) >= 1:
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ibmax = '--bmax %s' % options.ibmax
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else:
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ibmax = ''
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if options.ibmaxdivn and int( options.ibmaxdivn ) >= 0:
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ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn
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else:
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ibmaxdivn = ''
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if options.idcv and int( options.idcv ) > 0:
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idcv = '--dcv %s' % options.idcv
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else:
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idcv = ''
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if options.inodc and options.inodc == 'nodc':
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inodc = '--nodc'
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else:
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inodc = ''
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if options.inoref and options.inoref == 'noref':
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inoref = '--noref'
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else:
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inoref = ''
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if options.iftab and int( options.iftab ) >= 0:
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iftab = '--ftabchars %s' % options.iftab
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else:
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iftab = ''
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if options.intoa and options.intoa == 'yes':
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intoa = '--ntoa'
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else:
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intoa = ''
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if options.iendian and options.iendian == 'big':
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iendian = '--big'
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else:
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iendian = '--little'
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if options.iseed and int( options.iseed ) > 0:
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iseed = '--seed %s' % options.iseed
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else:
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iseed = ''
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if options.icutoff and int( options.icutoff ) > 0:
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icutoff = '--cutoff %s' % options.icutoff
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else:
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icutoff = ''
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indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \
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( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc,
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inoref, options.ioffrate, iftab, intoa, iendian,
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iseed, icutoff, colorspace )
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except ValueError, e:
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# clean up temp dir
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if os.path.exists( tmp_index_dir ):
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shutil.rmtree( tmp_index_dir )
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stop_err( "Something is wrong with the indexing parameters and the indexing and alignment could not be run. Make sure you don't have any non-numeric values where they should be numeric.\n" + str( e ) )
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ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
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ref_file_name = ref_file.name
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ref_file.close()
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os.symlink( options.ref, ref_file_name )
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cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name )
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try:
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tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
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tmp_stderr = open( tmp, 'wb' )
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proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_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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buffsize = 1048576
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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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# clean up temp dir
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if os.path.exists( tmp_index_dir ):
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shutil.rmtree( tmp_index_dir )
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stop_err( 'Error indexing reference sequence\n' + str( e ) )
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stdout += 'File indexed. '
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else:
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ref_file_name = options.ref
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# set up aligning and generate aligning command options
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# automatically set threads in both cases
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tmp_suppressed_file_name = None
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tmp_unmapped_file_name = None
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if options.suppressHeader == 'true':
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suppressHeader = '--sam-nohead'
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else:
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suppressHeader = ''
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if options.maxInsert and int( options.maxInsert ) > 0:
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maxInsert = '-X %s' % options.maxInsert
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else:
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maxInsert = ''
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if options.mateOrient:
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mateOrient = '--%s' % options.mateOrient
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else:
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mateOrient = ''
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quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING )
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if options.params == 'preSet':
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aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \
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( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding )
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else:
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try:
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if options.skip and int( options.skip ) > 0:
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skip = '-s %s' % options.skip
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else:
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skip = ''
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if options.alignLimit and int( options.alignLimit ) >= 0:
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alignLimit = '-u %s' % options.alignLimit
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else:
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alignLimit = ''
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if options.trimH and int( options.trimH ) > 0:
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trimH = '-5 %s' % options.trimH
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else:
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trimH = ''
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if options.trimL and int( options.trimL ) > 0:
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trimL = '-3 %s' % options.trimL
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else:
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trimL = ''
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if options.maqSoapAlign != '-1' and int( options.maqSoapAlign ) >= 0:
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maqSoapAlign = '-v %s' % options.maqSoapAlign
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else:
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maqSoapAlign = ''
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if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \
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or options.mismatchSeed == '2' or options.mismatchSeed == '3'):
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mismatchSeed = '-n %s' % options.mismatchSeed
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else:
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mismatchSeed = ''
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if options.mismatchQual and int( options.mismatchQual ) >= 0:
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mismatchQual = '-e %s' % options.mismatchQual
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else:
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mismatchQual = ''
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if options.seedLen and int( options.seedLen ) >= 5:
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seedLen = '-l %s' % options.seedLen
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else:
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seedLen = ''
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if options.rounding == 'noRound':
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rounding = '--nomaqround'
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else:
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rounding = ''
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if options.minInsert and int( options.minInsert ) > 0:
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minInsert = '-I %s' % options.minInsert
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else:
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minInsert = ''
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if options.maxAlignAttempt and int( options.maxAlignAttempt ) >= 0:
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maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt
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else:
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maxAlignAttempt = ''
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if options.forwardAlign == 'noForward':
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forwardAlign = '--nofw'
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else:
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forwardAlign = ''
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if options.reverseAlign == 'noReverse':
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reverseAlign = '--norc'
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else:
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reverseAlign = ''
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if options.maxBacktracks and int( options.maxBacktracks ) > 0 and \
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( options.mismatchSeed == '2' or options.mismatchSeed == '3' ):
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maxBacktracks = '--maxbts %s' % options.maxBacktracks
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else:
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maxBacktracks = ''
|
|
if options.tryHard == 'doTryHard':
|
|
tryHard = '-y'
|
|
else:
|
|
tryHard = ''
|
|
if options.valAlign and int( options.valAlign ) >= 0:
|
|
valAlign = '-k %s' % options.valAlign
|
|
else:
|
|
valAlign = ''
|
|
if options.allValAligns == 'doAllValAligns':
|
|
allValAligns = '-a'
|
|
else:
|
|
allValAligns = ''
|
|
if options.suppressAlign and int( options.suppressAlign ) >= 0:
|
|
suppressAlign = '-m %s' % options.suppressAlign
|
|
else:
|
|
suppressAlign = ''
|
|
if options.best == 'doBest':
|
|
best = '--best'
|
|
else:
|
|
best = ''
|
|
if options.strata == 'doStrata':
|
|
strata = '--strata'
|
|
else:
|
|
strata = ''
|
|
if options.offrate and int( options.offrate ) >= 0:
|
|
offrate = '-o %s' % options.offrate
|
|
else:
|
|
offrate = ''
|
|
if options.seed and int( options.seed ) >= 0:
|
|
seed = '--seed %s' % options.seed
|
|
else:
|
|
seed = ''
|
|
if options.paired == 'paired':
|
|
if options.output_unmapped_reads_l and options.output_unmapped_reads_r:
|
|
tmp_unmapped_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
|
|
tmp_unmapped_file_name = tmp_unmapped_file.name
|
|
tmp_unmapped_file.close()
|
|
output_unmapped_reads = '--un %s' % tmp_unmapped_file_name
|
|
else:
|
|
output_unmapped_reads = ''
|
|
if options.output_suppressed_reads:
|
|
tmp_suppressed_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
|
|
tmp_suppressed_file_name = tmp_suppressed_file.name
|
|
tmp_suppressed_file.close()
|
|
output_suppressed_reads = '--max %s' % tmp_suppressed_file_name
|
|
else:
|
|
output_suppressed_reads = ''
|
|
else:
|
|
if options.output_unmapped_reads:
|
|
output_unmapped_reads = '--un %s' % options.output_unmapped_reads
|
|
else:
|
|
output_unmapped_reads = ''
|
|
if options.output_suppressed_reads:
|
|
output_suppressed_reads = '--max %s' % options.output_suppressed_reads
|
|
else:
|
|
output_suppressed_reads = ''
|
|
snpfrac = ''
|
|
if options.snpphred and int( options.snpphred ) >= 0:
|
|
snpphred = '--snpphred %s' % options.snpphred
|
|
else:
|
|
snpphred = ''
|
|
if options.snpfrac and float( options.snpfrac ) >= 0:
|
|
snpfrac = '--snpfrac %s' % options.snpfrac
|
|
if options.keepends and options.keepends == 'doKeepends':
|
|
keepends = '--col-keepends'
|
|
else:
|
|
keepends = ''
|
|
aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \
|
|
'%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \
|
|
( maxInsert, mateOrient, options.threads, suppressHeader,
|
|
colorspace, skip, alignLimit, trimH, trimL, maqSoapAlign,
|
|
mismatchSeed, mismatchQual, seedLen, rounding, minInsert,
|
|
maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,
|
|
tryHard, valAlign, allValAligns, suppressAlign, best,
|
|
strata, offrate, seed, snpphred, snpfrac, keepends,
|
|
output_unmapped_reads, output_suppressed_reads,
|
|
quality_score_encoding )
|
|
except ValueError, e:
|
|
# clean up temp dir
|
|
if os.path.exists( tmp_index_dir ):
|
|
shutil.rmtree( tmp_index_dir )
|
|
stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) )
|
|
try:
|
|
# have to nest try-except in try-finally to handle 2.4
|
|
try:
|
|
# prepare actual mapping commands
|
|
if options.paired == 'paired':
|
|
cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
|
|
else:
|
|
cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
|
|
# align
|
|
tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
|
|
tmp_stderr = open( tmp, 'wb' )
|
|
proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, 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()
|
|
if returncode != 0:
|
|
raise Exception, stderr
|
|
# get suppressed and unmapped reads output files in place if appropriate
|
|
if options.paired == 'paired' and tmp_suppressed_file_name and \
|
|
options.output_suppressed_reads_l and options.output_suppressed_reads_r:
|
|
try:
|
|
left = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
|
|
right = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
|
|
shutil.move( left, options.output_suppressed_reads_l )
|
|
shutil.move( right, options.output_suppressed_reads_r )
|
|
except Exception, e:
|
|
sys.stdout.write( 'Error producing the suppressed output file.\n' )
|
|
if options.paired == 'paired' and tmp_unmapped_file_name and \
|
|
options.output_unmapped_reads_l and options.output_unmapped_reads_r:
|
|
try:
|
|
left = tmp_unmapped_file_name.replace( '.fastq', '_1.fastq' )
|
|
right = tmp_unmapped_file_name.replace( '.fastq', '_2.fastq' )
|
|
shutil.move( left, options.output_unmapped_reads_l )
|
|
shutil.move( right, options.output_unmapped_reads_r )
|
|
except Exception, e:
|
|
sys.stdout.write( 'Error producing the unmapped output file.\n' )
|
|
# check that there are results in the output file
|
|
if os.path.getsize( options.output ) == 0:
|
|
raise Exception, 'The output file is empty, there may be an error with your input file or settings.'
|
|
except Exception, e:
|
|
stop_err( 'Error aligning sequence. ' + str( e ) )
|
|
finally:
|
|
# clean up temp dir
|
|
if os.path.exists( tmp_index_dir ):
|
|
shutil.rmtree( tmp_index_dir )
|
|
stdout += 'Sequence file aligned.\n'
|
|
sys.stdout.write( stdout )
|
|
|
|
if __name__=="__main__": __main__()
|