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1
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1 #!/usr/bin/env python
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2
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3 """
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4 Runs Bowtie on single-end or paired-end data.
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5
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6 usage: bowtie_wrapper.py [options]
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7 -t, --threads=t: The number of threads to run
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8 -o, --output=o: The output file
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9 --output_unmapped_reads=: File name for unmapped reads (single-end)
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10 --output_unmapped_reads_l=: File name for unmapped reads (left, paired-end)
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11 --output_unmapped_reads_r=: File name for unmapped reads (right, paired-end)
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12 --output_suppressed_reads=: File name for suppressed reads because of max setting (single-end)
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13 --output_suppressed_reads_l=: File name for suppressed reads because of max setting (left, paired-end)
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14 --output_suppressed_reads_r=: File name for suppressed reads because of max setting (right, paired-end)
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15 --output_mapping_stats=: File name for mapping statistics (output on stderr by bowtie)
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16 -i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format
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17 -I, --input2=I: The reverse reads file in Sanger FASTQ format
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18 -4, --dataType=4: The type of data (SOLiD or Solexa)
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19 -2, --paired=2: Whether the data is single- or paired-end
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20 -g, --genomeSource=g: The type of reference provided
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21 -r, --ref=r: The reference genome to use or index
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22 -s, --skip=s: Skip the first n reads
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23 -a, --alignLimit=a: Only align the first n reads
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24 -T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment
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25 -L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment
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26 -m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed
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27 -M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions
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28 -l, --seedLen=l: Seed length
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29 -n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30
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30 -P, --maxMismatches=P: Maximum number of mismatches for -v alignment mode
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31 -w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist
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32 -V, --allValAligns=V: Whether or not to report all valid alignments per read or pair
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33 -v, --valAlign=v: Report up to n valid alignments per read or pair
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34 -G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist
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35 -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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36 -B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read
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37 -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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38 -j, --minInsert=j: Minimum insert size for valid paired-end alignments
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39 -J, --maxInsert=J: Maximum insert size for valid paired-end alignments
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40 -O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand
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41 -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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42 -f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand
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43 -E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand
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44 -F, --offrate=F: Override the offrate of the index to n
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45 -8, --snpphred=8: SNP penalty on Phred scale
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46 -6, --snpfrac=6: Fraction of sites expected to be SNP sites
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47 -7, --keepends=7: Keep extreme-end nucleotides and qualities
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48 -S, --seed=S: Seed for pseudo-random number generator
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49 -C, --params=C: Whether to use default or specified parameters
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50 -u, --iautoB=u: Automatic or specified behavior
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51 -K, --ipacked=K: Whether or not to use a packed representation for DNA strings
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52 -Q, --ibmax=Q: Maximum number of suffixes allowed in a block
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53 -Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference
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54 -D, --idcv=D: The period for the difference-cover sample
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55 -U, --inodc=U: Whether or not to disable the use of the difference-cover sample
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56 -y, --inoref=y: Whether or not to build the part of the reference index used only in paired-end alignment
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57 -z, --ioffrate=z: How many rows get marked during annotation of some or all of the Burrows-Wheeler rows
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58 -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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59 -X, --intoa=X: Whether or not to convert Ns in the reference sequence to As
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60 -N, --iendian=N: Endianness to use when serializing integers to the index file
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61 -Z, --iseed=Z: Seed for the pseudorandom number generator
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62 -x, --indexSettings=x: Whether or not indexing options are to be set
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63 -H, --suppressHeader=H: Suppress header
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64 --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
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65 """
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66
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67 import optparse
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68 import os
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69 import shutil
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70 import subprocess
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71 import sys
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72 import tempfile
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73
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74 # Allow more than Sanger encoded variants
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75 DEFAULT_ASCII_ENCODING = '--phred33-quals'
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76 GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = {'fastqsanger': '--phred33-quals', 'fastqillumina': '--phred64-quals', 'fastqsolexa': '--solexa-quals'}
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77 # 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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78
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79
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80 def stop_err( msg ):
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81 sys.exit('%s\n' % msg)
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82
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83
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84 def __main__():
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85 parser = optparse.OptionParser()
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86 parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to run' )
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87 parser.add_option( '-o', '--output', dest='output', help='The output file' )
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88 parser.add_option( '', '--output_unmapped_reads', dest='output_unmapped_reads', help='File name for unmapped reads (single-end)' )
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89 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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90 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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91 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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92 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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93 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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94 parser.add_option( '', '--output_mapping_stats', dest='output_mapping_stats', help='File for mapping statistics (i.e. stderr from bowtie)' )
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95 parser.add_option( '-4', '--dataType', dest='dataType', help='The type of data (SOLiD or Solexa)' )
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96 parser.add_option( '-i', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
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97 parser.add_option( '-I', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
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98 parser.add_option( '-2', '--paired', dest='paired', help='Whether the data is single- or paired-end' )
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99 parser.add_option( '-g', '--genomeSource', dest='genomeSource', help='The type of reference provided' )
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100 parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' )
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101 parser.add_option( '-s', '--skip', dest='skip', help='Skip the first n reads' )
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102 parser.add_option( '-a', '--alignLimit', dest='alignLimit', help='Only align the first n reads' )
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103 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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104 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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105 parser.add_option( '-m', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed' )
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106 parser.add_option( '-M', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions' )
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107 parser.add_option( '-l', '--seedLen', dest='seedLen', help='Seed length' )
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108 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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109 parser.add_option( '-P', '--maxMismatches', dest='maxMismatches', help='Maximum number of mismatches for -v alignment mode' )
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110 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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111 parser.add_option( '-V', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read or pair' )
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112 parser.add_option( '-v', '--valAlign', dest='valAlign', help='Report up to n valid alignments per read or pair' )
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113 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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114 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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115 parser.add_option( '-B', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read' )
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116 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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117 parser.add_option( '-j', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments' )
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118 parser.add_option( '-J', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments' )
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119 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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120 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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121 parser.add_option( '-f', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand' )
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122 parser.add_option( '-E', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand' )
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123 parser.add_option( '-F', '--offrate', dest='offrate', help='Override the offrate of the index to n' )
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124 parser.add_option( '-S', '--seed', dest='seed', help='Seed for pseudo-random number generator' )
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125 parser.add_option( '-8', '--snpphred', dest='snpphred', help='SNP penalty on Phred scale' )
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126 parser.add_option( '-6', '--snpfrac', dest='snpfrac', help='Fraction of sites expected to be SNP sites' )
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127 parser.add_option( '-7', '--keepends', dest='keepends', help='Keep extreme-end nucleotides and qualities' )
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128 parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' )
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129 parser.add_option( '-u', '--iautoB', dest='iautoB', help='Automatic or specified behavior' )
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130 parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' )
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131 parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' )
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132 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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133 parser.add_option( '-D', '--idcv', dest='idcv', help='The period for the difference-cover sample' )
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134 parser.add_option( '-U', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample' )
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135 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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136 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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137 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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138 parser.add_option( '-X', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As' )
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139 parser.add_option( '-N', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file' )
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140 parser.add_option( '-Z', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator' )
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141 parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' )
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142 parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
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143 parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fastqsanger", help='galaxy input format' )
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144 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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145 (options, args) = parser.parse_args()
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146 if options.mismatchSeed and options.maxMismatches:
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147 parser.error("options --mismatchSeed and --maxMismatches are mutually exclusive")
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148 stdout = ''
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149
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150 # make temp directory for placement of indices and copy reference file there if necessary
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151 tmp_index_dir = tempfile.mkdtemp()
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152 # get type of data (solid or solexa)
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153 if options.dataType == 'solid':
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154 colorspace = '-C'
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155 else:
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156 colorspace = ''
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157 # index if necessary
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158 if options.genomeSource == 'history' and not options.do_not_build_index:
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159 # set up commands
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160 if options.index_settings == 'indexPreSet':
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161 indexing_cmds = '%s' % colorspace
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162 else:
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163 try:
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164 if options.iautoB and options.iautoB == 'set':
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165 iautoB = '--noauto'
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166 else:
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167 iautoB = ''
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168 if options.ipacked and options.ipacked == 'packed':
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169 ipacked = '--packed'
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170 else:
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171 ipacked = ''
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172 if options.ibmax and int( options.ibmax ) >= 1:
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173 ibmax = '--bmax %s' % options.ibmax
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174 else:
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175 ibmax = ''
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176 if options.ibmaxdivn and int( options.ibmaxdivn ) >= 0:
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177 ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn
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178 else:
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179 ibmaxdivn = ''
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180 if options.idcv and int( options.idcv ) >= 3:
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181 idcv = '--dcv %s' % options.idcv
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182 else:
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183 idcv = ''
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184 if options.inodc and options.inodc == 'nodc':
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185 inodc = '--nodc'
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186 else:
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187 inodc = ''
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188 if options.inoref and options.inoref == 'noref':
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189 inoref = '--noref'
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190 else:
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191 inoref = ''
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192 if options.iftab and int( options.iftab ) >= 1:
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193 iftab = '--ftabchars %s' % options.iftab
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194 else:
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195 iftab = ''
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196 if options.intoa and options.intoa == 'yes':
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197 intoa = '--ntoa'
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198 else:
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199 intoa = ''
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200 if options.iendian and options.iendian == 'big':
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201 iendian = '--big'
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202 else:
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203 iendian = '--little'
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204 if options.iseed and int( options.iseed ) > 0:
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205 iseed = '--seed %s' % options.iseed
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206 else:
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207 iseed = ''
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208 indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s' % \
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209 ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc,
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210 inoref, options.ioffrate, iftab, intoa, iendian,
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211 iseed, colorspace )
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212 except ValueError as e:
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213 # clean up temp dir
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214 if os.path.exists( tmp_index_dir ):
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215 shutil.rmtree( tmp_index_dir )
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216 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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217 ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
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218 ref_file_name = ref_file.name
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219 ref_file.close()
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220 os.symlink( options.ref, ref_file_name )
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221 cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name )
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222 try:
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223 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
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224 with open(tmp, 'w') as tmp_stderr:
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225 returncode = subprocess.call(args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno())
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226 if returncode != 0:
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227 # get stderr, allowing for case where it's very large
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228 stderr = ''
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229 buffsize = 1048576
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230 with open(tmp, 'r') as tmp_stderr:
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231 try:
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232 while True:
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233 stderr += tmp_stderr.read(buffsize)
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234 if not stderr or len(stderr) % buffsize != 0:
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235 break
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236 except OverflowError:
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237 pass
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238 raise Exception(stderr)
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239 except Exception as e:
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240 # clean up temp dir
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241 if os.path.exists( tmp_index_dir ):
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242 shutil.rmtree( tmp_index_dir )
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243 stop_err( 'Error indexing reference sequence\n' + str( e ) )
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244 stdout += 'File indexed. '
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245 else:
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246 ref_file_name = options.ref
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247 # set up aligning and generate aligning command options
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248 # automatically set threads in both cases
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249 tmp_suppressed_file_name = None
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250 tmp_unmapped_file_name = None
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251 if options.suppressHeader == 'true':
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252 suppressHeader = '--sam-nohead'
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253 else:
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254 suppressHeader = ''
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255 if options.maxInsert and int( options.maxInsert ) > 0:
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256 maxInsert = '-X %s' % options.maxInsert
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257 else:
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258 maxInsert = ''
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259 if options.mateOrient:
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260 mateOrient = '--%s' % options.mateOrient
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261 else:
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262 mateOrient = ''
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263 quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING )
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264 if options.params == 'preSet':
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265 aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \
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266 ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding )
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267 else:
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268 try:
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269 if options.skip and int( options.skip ) > 0:
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270 skip = '-s %s' % options.skip
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271 else:
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272 skip = ''
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273 if options.alignLimit and int( options.alignLimit ) >= 0:
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274 alignLimit = '-u %s' % options.alignLimit
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275 else:
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276 alignLimit = ''
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277 if options.trimH and int( options.trimH ) > 0:
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278 trimH = '-5 %s' % options.trimH
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279 else:
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280 trimH = ''
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281 if options.trimL and int( options.trimL ) > 0:
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282 trimL = '-3 %s' % options.trimL
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283 else:
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284 trimL = ''
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285 if options.maxMismatches and (options.maxMismatches == '0' or options.maxMismatches == '1' or
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286 options.maxMismatches == '2' or options.maxMismatches == '3'):
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287 maxMismatches = '-v %s' % options.maxMismatches
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288 else:
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289 maxMismatches = ''
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290 if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' or
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291 options.mismatchSeed == '2' or options.mismatchSeed == '3'):
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292 mismatchSeed = '-n %s' % options.mismatchSeed
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293 else:
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294 mismatchSeed = ''
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295 if options.mismatchQual and int( options.mismatchQual ) >= 1:
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296 mismatchQual = '-e %s' % options.mismatchQual
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297 else:
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298 mismatchQual = ''
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299 if options.seedLen and int( options.seedLen ) >= 5:
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300 seedLen = '-l %s' % options.seedLen
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301 else:
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302 seedLen = ''
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303 if options.rounding == 'noRound':
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304 rounding = '--nomaqround'
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305 else:
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306 rounding = ''
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307 if options.minInsert and int( options.minInsert ) > 0:
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308 minInsert = '-I %s' % options.minInsert
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309 else:
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310 minInsert = ''
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311 if options.maxAlignAttempt and int( options.maxAlignAttempt ) >= 0:
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312 maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt
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313 else:
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314 maxAlignAttempt = ''
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315 if options.forwardAlign == 'noForward':
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316 forwardAlign = '--nofw'
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317 else:
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318 forwardAlign = ''
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319 if options.reverseAlign == 'noReverse':
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320 reverseAlign = '--norc'
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321 else:
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322 reverseAlign = ''
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323 if options.maxBacktracks and int( options.maxBacktracks ) > 0 and \
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324 ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ):
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325 maxBacktracks = '--maxbts %s' % options.maxBacktracks
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326 else:
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327 maxBacktracks = ''
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328 if options.tryHard == 'doTryHard':
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329 tryHard = '-y'
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330 else:
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331 tryHard = ''
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332 if options.valAlign and int( options.valAlign ) >= 0:
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333 valAlign = '-k %s' % options.valAlign
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334 else:
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335 valAlign = ''
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336 if options.allValAligns == 'doAllValAligns':
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337 allValAligns = '-a'
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338 else:
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339 allValAligns = ''
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340 if options.suppressAlign and int( options.suppressAlign ) >= 0:
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|
341 suppressAlign = '-m %s' % options.suppressAlign
|
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342 else:
|
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|
343 suppressAlign = ''
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|
344 if options.best == 'doBest':
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|
345 best = '--best'
|
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|
346 else:
|
|
|
347 best = ''
|
|
|
348 if options.strata == 'doStrata':
|
|
|
349 strata = '--strata'
|
|
|
350 else:
|
|
|
351 strata = ''
|
|
|
352 if options.offrate and int( options.offrate ) >= 0:
|
|
|
353 offrate = '-o %s' % options.offrate
|
|
|
354 else:
|
|
|
355 offrate = ''
|
|
|
356 if options.seed and int( options.seed ) >= 0:
|
|
|
357 seed = '--seed %s' % options.seed
|
|
|
358 else:
|
|
|
359 seed = ''
|
|
|
360 if options.paired == 'paired':
|
|
|
361 if options.output_unmapped_reads_l and options.output_unmapped_reads_r:
|
|
|
362 tmp_unmapped_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
|
|
|
363 tmp_unmapped_file_name = tmp_unmapped_file.name
|
|
|
364 tmp_unmapped_file.close()
|
|
|
365 output_unmapped_reads = '--un %s' % tmp_unmapped_file_name
|
|
|
366 else:
|
|
|
367 output_unmapped_reads = ''
|
|
|
368 if options.output_suppressed_reads:
|
|
|
369 tmp_suppressed_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
|
|
|
370 tmp_suppressed_file_name = tmp_suppressed_file.name
|
|
|
371 tmp_suppressed_file.close()
|
|
|
372 output_suppressed_reads = '--max %s' % tmp_suppressed_file_name
|
|
|
373 else:
|
|
|
374 output_suppressed_reads = ''
|
|
|
375 else:
|
|
|
376 if options.output_unmapped_reads:
|
|
|
377 output_unmapped_reads = '--un %s' % options.output_unmapped_reads
|
|
|
378 else:
|
|
|
379 output_unmapped_reads = ''
|
|
|
380 if options.output_suppressed_reads:
|
|
|
381 output_suppressed_reads = '--max %s' % options.output_suppressed_reads
|
|
|
382 else:
|
|
|
383 output_suppressed_reads = ''
|
|
|
384 snpfrac = ''
|
|
|
385 if options.snpphred and int( options.snpphred ) >= 0:
|
|
|
386 snpphred = '--snpphred %s' % options.snpphred
|
|
|
387 else:
|
|
|
388 snpphred = ''
|
|
|
389 if options.snpfrac and float( options.snpfrac ) >= 0:
|
|
|
390 snpfrac = '--snpfrac %s' % options.snpfrac
|
|
|
391 if options.keepends and options.keepends == 'doKeepends':
|
|
|
392 keepends = '--col-keepends'
|
|
|
393 else:
|
|
|
394 keepends = ''
|
|
|
395 aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \
|
|
|
396 '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \
|
|
|
397 ( maxInsert, mateOrient, options.threads, suppressHeader,
|
|
|
398 colorspace, skip, alignLimit, trimH, trimL, maxMismatches,
|
|
|
399 mismatchSeed, mismatchQual, seedLen, rounding, minInsert,
|
|
|
400 maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,
|
|
|
401 tryHard, valAlign, allValAligns, suppressAlign, best,
|
|
|
402 strata, offrate, seed, snpphred, snpfrac, keepends,
|
|
|
403 output_unmapped_reads, output_suppressed_reads,
|
|
|
404 quality_score_encoding )
|
|
|
405 except ValueError as e:
|
|
|
406 # clean up temp dir
|
|
|
407 if os.path.exists( tmp_index_dir ):
|
|
|
408 shutil.rmtree( tmp_index_dir )
|
|
|
409 stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) )
|
|
|
410 try:
|
|
|
411 # have to nest try-except in try-finally to handle 2.4
|
|
|
412 try:
|
|
|
413 # prepare actual mapping commands
|
|
|
414 if options.paired == 'paired':
|
|
8
|
415 # cmd2 = 'bowtie %s %s -1 %s -2 %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output, options.output )
|
|
|
416 cmd2 = 'bowtie %s %s -1 %s -2 %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
|
|
|
417
|
|
1
|
418 else:
|
|
8
|
419 # cmd2 = 'bowtie %s %s %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output, options.output )
|
|
|
420 cmd2 = 'bowtie %s %s %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.output )
|
|
|
421
|
|
1
|
422 # align
|
|
|
423 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
|
|
|
424 with open(tmp, 'w') as tmp_stderr:
|
|
|
425 returncode = subprocess.call(args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno())
|
|
|
426 # get stderr, allowing for case where it's very large
|
|
|
427 stderr = ''
|
|
|
428 buffsize = 1048576
|
|
|
429 with open(tmp, 'r') as tmp_stderr:
|
|
|
430 try:
|
|
|
431 while True:
|
|
|
432 stderr += tmp_stderr.read(buffsize)
|
|
|
433 if not stderr or len(stderr) % buffsize != 0:
|
|
|
434 break
|
|
|
435 except OverflowError:
|
|
|
436 pass
|
|
|
437 if returncode != 0:
|
|
|
438 raise Exception(stderr)
|
|
|
439 elif options.output_mapping_stats is not None:
|
|
|
440 # Write stderr (containing the mapping statistics) to a named file
|
|
|
441 with open(options.output_mapping_stats, 'w') as mapping_stats:
|
|
|
442 mapping_stats.write( stderr )
|
|
|
443 # get suppressed and unmapped reads output files in place if appropriate
|
|
|
444 if options.paired == 'paired' and tmp_suppressed_file_name and \
|
|
|
445 options.output_suppressed_reads_l and options.output_suppressed_reads_r:
|
|
|
446 try:
|
|
|
447 left = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
|
|
|
448 right = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
|
|
|
449 shutil.move( left, options.output_suppressed_reads_l )
|
|
|
450 shutil.move( right, options.output_suppressed_reads_r )
|
|
|
451 except Exception as e:
|
|
|
452 sys.stdout.write( 'Error producing the suppressed output file.\n' )
|
|
|
453 if options.paired == 'paired' and tmp_unmapped_file_name and \
|
|
|
454 options.output_unmapped_reads_l and options.output_unmapped_reads_r:
|
|
|
455 try:
|
|
|
456 left = tmp_unmapped_file_name.replace( '.fastq', '_1.fastq' )
|
|
|
457 right = tmp_unmapped_file_name.replace( '.fastq', '_2.fastq' )
|
|
|
458 shutil.move( left, options.output_unmapped_reads_l )
|
|
|
459 shutil.move( right, options.output_unmapped_reads_r )
|
|
|
460 except Exception as e:
|
|
|
461 sys.stdout.write( 'Error producing the unmapped output file.\n' )
|
|
|
462 # check that there are results in the output file
|
|
|
463 if os.path.getsize( options.output ) == 0:
|
|
|
464 raise Exception('The output file is empty, there may be an error with your input file or settings.')
|
|
|
465 except Exception as e:
|
|
|
466 stop_err( 'Error aligning sequence. ' + str( e ) )
|
|
|
467 finally:
|
|
|
468 # clean up temp dir
|
|
|
469 if os.path.exists( tmp_index_dir ):
|
|
|
470 shutil.rmtree( tmp_index_dir )
|
|
|
471 stdout += 'Sequence file aligned.\n'
|
|
|
472 sys.stdout.write( stdout )
|
|
|
473
|
|
|
474
|
|
|
475 if __name__ == "__main__":
|
|
|
476 __main__()
|
