--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py	Tue Mar 22 12:34:36 2022 +0000
@@ -0,0 +1,472 @@
+#!/usr/bin/env python
+
+"""
+Runs Bowtie on single-end or paired-end data.
+
+usage: bowtie_wrapper.py [options]
+    -t, --threads=t: The number of threads to run
+    -o, --output=o: The output file
+    --output_unmapped_reads=: File name for unmapped reads (single-end)
+    --output_unmapped_reads_l=: File name for unmapped reads (left, paired-end)
+    --output_unmapped_reads_r=: File name for unmapped reads (right, paired-end)
+    --output_suppressed_reads=: File name for suppressed reads because of max setting (single-end)
+    --output_suppressed_reads_l=: File name for suppressed reads because of max setting (left, paired-end)
+    --output_suppressed_reads_r=: File name for suppressed reads because of max setting (right, paired-end)
+    --output_mapping_stats=: File name for mapping statistics (output on stderr by bowtie)
+    -i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format
+    -I, --input2=I: The reverse reads file in Sanger FASTQ format
+    -4, --dataType=4: The type of data (SOLiD or Solexa)
+    -2, --paired=2: Whether the data is single- or paired-end
+    -g, --genomeSource=g: The type of reference provided
+    -r, --ref=r: The reference genome to use or index
+    -s, --skip=s: Skip the first n reads
+    -a, --alignLimit=a: Only align the first n reads
+    -T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment
+    -L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment
+    -m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed
+    -M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions
+    -l, --seedLen=l: Seed length
+    -n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30
+    -P, --maxMismatches=P: Maximum number of mismatches for -v alignment mode
+    -w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist
+    -V, --allValAligns=V: Whether or not to report all valid alignments per read or pair
+    -v, --valAlign=v: Report up to n valid alignments per read or pair
+    -G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist
+    -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
+    -B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read
+    -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
+    -j, --minInsert=j: Minimum insert size for valid paired-end alignments
+    -J, --maxInsert=J: Maximum insert size for valid paired-end alignments
+    -O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand
+    -A, --maxAlignAttempt=A: Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate
+    -f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand
+    -E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand
+    -F, --offrate=F: Override the offrate of the index to n
+    -8, --snpphred=8: SNP penalty on Phred scale
+    -6, --snpfrac=6: Fraction of sites expected to be SNP sites
+    -7, --keepends=7: Keep extreme-end nucleotides and qualities
+    -S, --seed=S: Seed for pseudo-random number generator
+    -C, --params=C: Whether to use default or specified parameters
+    -u, --iautoB=u: Automatic or specified behavior
+    -K, --ipacked=K: Whether or not to use a packed representation for DNA strings
+    -Q, --ibmax=Q: Maximum number of suffixes allowed in a block
+    -Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference
+    -D, --idcv=D: The period for the difference-cover sample
+    -U, --inodc=U: Whether or not to disable the use of the difference-cover sample
+    -y, --inoref=y: Whether or not to build the part of the reference index used only in paired-end alignment
+    -z, --ioffrate=z: How many rows get marked during annotation of some or all of the Burrows-Wheeler rows
+    -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
+    -X, --intoa=X: Whether or not to convert Ns in the reference sequence to As
+    -N, --iendian=N: Endianness to use when serializing integers to the index file
+    -Z, --iseed=Z: Seed for the pseudorandom number generator
+    -x, --indexSettings=x: Whether or not indexing options are to be set
+    -H, --suppressHeader=H: Suppress header
+    --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
+"""
+
+import optparse
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+
+# Allow more than Sanger encoded variants
+DEFAULT_ASCII_ENCODING = '--phred33-quals'
+GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = {'fastqsanger': '--phred33-quals', 'fastqillumina': '--phred64-quals', 'fastqsolexa': '--solexa-quals'}
+# 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
+
+
+def stop_err( msg ):
+    sys.exit('%s\n' % msg)
+
+
+def __main__():
+    parser = optparse.OptionParser()
+    parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to run' )
+    parser.add_option( '-o', '--output', dest='output', help='The output file' )
+    parser.add_option( '', '--output_unmapped_reads', dest='output_unmapped_reads', help='File name for unmapped reads (single-end)' )
+    parser.add_option( '', '--output_unmapped_reads_l', dest='output_unmapped_reads_l', help='File name for unmapped reads (left, paired-end)' )
+    parser.add_option( '', '--output_unmapped_reads_r', dest='output_unmapped_reads_r', help='File name for unmapped reads (right, paired-end)' )
+    parser.add_option( '', '--output_suppressed_reads', dest='output_suppressed_reads', help='File name for suppressed reads because of max setting (single-end)' )
+    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)' )
+    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)' )
+    parser.add_option( '', '--output_mapping_stats', dest='output_mapping_stats', help='File for mapping statistics (i.e. stderr from bowtie)' )
+    parser.add_option( '-4', '--dataType', dest='dataType', help='The type of data (SOLiD or Solexa)' )
+    parser.add_option( '-i', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
+    parser.add_option( '-I', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
+    parser.add_option( '-2', '--paired', dest='paired', help='Whether the data is single- or paired-end' )
+    parser.add_option( '-g', '--genomeSource', dest='genomeSource', help='The type of reference provided' )
+    parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' )
+    parser.add_option( '-s', '--skip', dest='skip', help='Skip the first n reads' )
+    parser.add_option( '-a', '--alignLimit', dest='alignLimit', help='Only align the first n reads' )
+    parser.add_option( '-T', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment' )
+    parser.add_option( '-L', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment' )
+    parser.add_option( '-m', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed' )
+    parser.add_option( '-M', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions' )
+    parser.add_option( '-l', '--seedLen', dest='seedLen', help='Seed length' )
+    parser.add_option( '-n', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30' )
+    parser.add_option( '-P', '--maxMismatches', dest='maxMismatches', help='Maximum number of mismatches for -v alignment mode' )
+    parser.add_option( '-w', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist' )
+    parser.add_option( '-V', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read or pair' )
+    parser.add_option( '-v', '--valAlign', dest='valAlign', help='Report up to n valid alignments per read or pair' )
+    parser.add_option( '-G', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist' )
+    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" )
+    parser.add_option( '-B', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read' )
+    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' )
+    parser.add_option( '-j', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments' )
+    parser.add_option( '-J', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments' )
+    parser.add_option( '-O', '--mateOrient', dest='mateOrient', help='The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand' )
+    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' )
+    parser.add_option( '-f', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand' )
+    parser.add_option( '-E', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand' )
+    parser.add_option( '-F', '--offrate', dest='offrate', help='Override the offrate of the index to n' )
+    parser.add_option( '-S', '--seed', dest='seed', help='Seed for pseudo-random number generator' )
+    parser.add_option( '-8', '--snpphred', dest='snpphred', help='SNP penalty on Phred scale' )
+    parser.add_option( '-6', '--snpfrac', dest='snpfrac', help='Fraction of sites expected to be SNP sites' )
+    parser.add_option( '-7', '--keepends', dest='keepends', help='Keep extreme-end nucleotides and qualities' )
+    parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' )
+    parser.add_option( '-u', '--iautoB', dest='iautoB', help='Automatic or specified behavior' )
+    parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' )
+    parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' )
+    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' )
+    parser.add_option( '-D', '--idcv', dest='idcv', help='The period for the difference-cover sample' )
+    parser.add_option( '-U', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample' )
+    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' )
+    parser.add_option( '-z', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows' )
+    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' )
+    parser.add_option( '-X', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As' )
+    parser.add_option( '-N', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file' )
+    parser.add_option( '-Z', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator' )
+    parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' )
+    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
+    parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fastqsanger", help='galaxy input format' )
+    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' )
+    (options, args) = parser.parse_args()
+    if options.mismatchSeed and options.maxMismatches:
+        parser.error("options --mismatchSeed and --maxMismatches are mutually exclusive")
+    stdout = ''
+
+    # make temp directory for placement of indices and copy reference file there if necessary
+    tmp_index_dir = tempfile.mkdtemp()
+    # get type of data (solid or solexa)
+    if options.dataType == 'solid':
+        colorspace = '-C'
+    else:
+        colorspace = ''
+    # index if necessary
+    if options.genomeSource == 'history' and not options.do_not_build_index:
+        # set up commands
+        if options.index_settings == 'indexPreSet':
+            indexing_cmds = '%s' % colorspace
+        else:
+            try:
+                if options.iautoB and options.iautoB == 'set':
+                    iautoB = '--noauto'
+                else:
+                    iautoB = ''
+                if options.ipacked and options.ipacked == 'packed':
+                    ipacked = '--packed'
+                else:
+                    ipacked = ''
+                if options.ibmax and int( options.ibmax ) >= 1:
+                    ibmax = '--bmax %s' % options.ibmax
+                else:
+                    ibmax = ''
+                if options.ibmaxdivn and int( options.ibmaxdivn ) >= 0:
+                    ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn
+                else:
+                    ibmaxdivn = ''
+                if options.idcv and int( options.idcv ) >= 3:
+                    idcv = '--dcv %s' % options.idcv
+                else:
+                    idcv = ''
+                if options.inodc and options.inodc == 'nodc':
+                    inodc = '--nodc'
+                else:
+                    inodc = ''
+                if options.inoref and options.inoref == 'noref':
+                    inoref = '--noref'
+                else:
+                    inoref = ''
+                if options.iftab and int( options.iftab ) >= 1:
+                    iftab = '--ftabchars %s' % options.iftab
+                else:
+                    iftab = ''
+                if options.intoa and options.intoa == 'yes':
+                    intoa = '--ntoa'
+                else:
+                    intoa = ''
+                if options.iendian and options.iendian == 'big':
+                    iendian = '--big'
+                else:
+                    iendian = '--little'
+                if options.iseed and int( options.iseed ) > 0:
+                    iseed = '--seed %s' % options.iseed
+                else:
+                    iseed = ''
+                indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s' % \
+                                ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc,
+                                  inoref, options.ioffrate, iftab, intoa, iendian,
+                                  iseed, colorspace )
+            except ValueError as e:
+                # clean up temp dir
+                if os.path.exists( tmp_index_dir ):
+                    shutil.rmtree( tmp_index_dir )
+                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 ) )
+        ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
+        ref_file_name = ref_file.name
+        ref_file.close()
+        os.symlink( options.ref, ref_file_name )
+        cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name )
+        try:
+            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
+            with open(tmp, 'w') as tmp_stderr:
+                returncode = subprocess.call(args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno())
+            if returncode != 0:
+                # get stderr, allowing for case where it's very large
+                stderr = ''
+                buffsize = 1048576
+                with open(tmp, 'r') as tmp_stderr:
+                    try:
+                        while True:
+                            stderr += tmp_stderr.read(buffsize)
+                            if not stderr or len(stderr) % buffsize != 0:
+                                break
+                    except OverflowError:
+                        pass
+                raise Exception(stderr)
+        except Exception as e:
+            # clean up temp dir
+            if os.path.exists( tmp_index_dir ):
+                shutil.rmtree( tmp_index_dir )
+            stop_err( 'Error indexing reference sequence\n' + str( e ) )
+        stdout += 'File indexed. '
+    else:
+        ref_file_name = options.ref
+    # set up aligning and generate aligning command options
+    # automatically set threads in both cases
+    tmp_suppressed_file_name = None
+    tmp_unmapped_file_name = None
+    if options.suppressHeader == 'true':
+        suppressHeader = '--sam-nohead'
+    else:
+        suppressHeader = ''
+    if options.maxInsert and int( options.maxInsert ) > 0:
+        maxInsert = '-X %s' % options.maxInsert
+    else:
+        maxInsert = ''
+    if options.mateOrient:
+        mateOrient = '--%s' % options.mateOrient
+    else:
+        mateOrient = ''
+    quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING )
+    if options.params == 'preSet':
+        aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \
+            ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding )
+    else:
+        try:
+            if options.skip and int( options.skip ) > 0:
+                skip = '-s %s' % options.skip
+            else:
+                skip = ''
+            if options.alignLimit and int( options.alignLimit ) >= 0:
+                alignLimit = '-u %s' % options.alignLimit
+            else:
+                alignLimit = ''
+            if options.trimH and int( options.trimH ) > 0:
+                trimH = '-5 %s' % options.trimH
+            else:
+                trimH = ''
+            if options.trimL and int( options.trimL ) > 0:
+                trimL = '-3 %s' % options.trimL
+            else:
+                trimL = ''
+            if options.maxMismatches and (options.maxMismatches == '0' or options.maxMismatches == '1' or
+                                          options.maxMismatches == '2' or options.maxMismatches == '3'):
+                maxMismatches = '-v %s' % options.maxMismatches
+            else:
+                maxMismatches = ''
+            if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' or
+                                         options.mismatchSeed == '2' or options.mismatchSeed == '3'):
+                mismatchSeed = '-n %s' % options.mismatchSeed
+            else:
+                mismatchSeed = ''
+            if options.mismatchQual and int( options.mismatchQual ) >= 1:
+                mismatchQual = '-e %s' % options.mismatchQual
+            else:
+                mismatchQual = ''
+            if options.seedLen and int( options.seedLen ) >= 5:
+                seedLen = '-l %s' % options.seedLen
+            else:
+                seedLen = ''
+            if options.rounding == 'noRound':
+                rounding = '--nomaqround'
+            else:
+                rounding = ''
+            if options.minInsert and int( options.minInsert ) > 0:
+                minInsert = '-I %s' % options.minInsert
+            else:
+                minInsert = ''
+            if options.maxAlignAttempt and int( options.maxAlignAttempt ) >= 0:
+                maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt
+            else:
+                maxAlignAttempt = ''
+            if options.forwardAlign == 'noForward':
+                forwardAlign = '--nofw'
+            else:
+                forwardAlign = ''
+            if options.reverseAlign == 'noReverse':
+                reverseAlign = '--norc'
+            else:
+                reverseAlign = ''
+            if options.maxBacktracks and int( options.maxBacktracks ) > 0 and \
+                    ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ):
+                maxBacktracks = '--maxbts %s' % options.maxBacktracks
+            else:
+                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, maxMismatches,
+                              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 as 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
+            with open(tmp, 'w') as tmp_stderr:
+                returncode = subprocess.call(args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno())
+            # get stderr, allowing for case where it's very large
+            stderr = ''
+            buffsize = 1048576
+            with open(tmp, 'r') as tmp_stderr:
+                try:
+                    while True:
+                        stderr += tmp_stderr.read(buffsize)
+                        if not stderr or len(stderr) % buffsize != 0:
+                            break
+                except OverflowError:
+                    pass
+            if returncode != 0:
+                raise Exception(stderr)
+            elif options.output_mapping_stats is not None:
+                # Write stderr (containing the mapping statistics) to a named file
+                with open(options.output_mapping_stats, 'w') as mapping_stats:
+                    mapping_stats.write( 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 as 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 as 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 as 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__()