# HG changeset patch # User mvdbeek # Date 1427639136 14400 # Node ID b50d7228b678498f3a23df5185226b8209a19d3c # Parent 64064dccdb116ea71470a3e5d8d6854d9d85344b Uploaded diff -r 64064dccdb11 -r b50d7228b678 sRbowtie.py --- a/sRbowtie.py Mon Nov 03 10:24:38 2014 -0500 +++ b/sRbowtie.py Sun Mar 29 10:25:36 2015 -0400 @@ -5,119 +5,185 @@ # current rev: for bowtie __norc, move from --supress 2,6,7,8 to --supress 6,7,8. Future Parser must be updated to take into account this standardisation # Christophe Antoniewski -import sys, os, subprocess, tempfile, shutil, argparse +import sys +import os +import subprocess +import tempfile +import shutil +import argparse + def Parser(): - the_parser = argparse.ArgumentParser(description="bowtie wrapper for small fasta reads") - the_parser.add_argument('--input', action="store", type=str, help="input fasta file") - the_parser.add_argument('--method', action="store", type=str, help="RNA, unique, multiple, k_option, n_option, a_option") - the_parser.add_argument('--v-mismatches', dest="v_mismatches", action="store", type=str, help="number of mismatches allowed for the alignments") - the_parser.add_argument('--output-format', dest="output_format", action="store", type=str, help="tabular, sam, bam") - the_parser.add_argument('--output', action="store", type=str, help="output file path") - the_parser.add_argument('--index-from', dest="index_from", action="store", type=str, help="indexed or history") - the_parser.add_argument('--index-source', dest="index_source", action="store", type=str, help="file path to the index source") - the_parser.add_argument('--aligned', action="store", type=str, help="aligned read file path, maybe None") - the_parser.add_argument('--unaligned', action="store", type=str, help="unaligned read file path, maybe None") - the_parser.add_argument('--num-threads', dest="num_threads", action="store", type=str, help="number of bowtie threads") - args = the_parser.parse_args() - return args + the_parser = argparse.ArgumentParser( + description="bowtie wrapper for small fasta reads") + the_parser.add_argument( + '--input', action="store", type=str, help="input file") + the_parser.add_argument( + '--input-format', dest="input_format", action="store", type=str, help="fasta or fastq") + the_parser.add_argument('--method', action="store", type=str, + help="RNA, unique, multiple, k_option, n_option, a_option") + the_parser.add_argument('--v-mismatches', dest="v_mismatches", action="store", + type=str, help="number of mismatches allowed for the alignments") + the_parser.add_argument( + '--output-format', dest="output_format", action="store", type=str, help="tabular, sam, bam") + the_parser.add_argument( + '--output', action="store", type=str, help="output file path") + the_parser.add_argument( + '--index-from', dest="index_from", action="store", type=str, help="indexed or history") + the_parser.add_argument('--index-source', dest="index_source", + action="store", type=str, help="file path to the index source") + the_parser.add_argument( + '--aligned', action="store", type=str, help="aligned read file path, maybe None") + the_parser.add_argument('--unaligned', action="store", + type=str, help="unaligned read file path, maybe None") + the_parser.add_argument('--num-threads', dest="num_threads", + action="store", type=str, help="number of bowtie threads") + args = the_parser.parse_args() + return args -def stop_err( msg ): - sys.stderr.write( '%s\n' % msg ) + +def stop_err(msg): + sys.stderr.write('%s\n' % msg) sys.exit() -def bowtieCommandLiner (alignment_method="RNA", v_mis="1", out_type="tabular", aligned="None", unaligned="None", input="path", index="path", output="path", pslots="4"): - if alignment_method=="RNA": - x = "-v %s -M 1 --best --strata -p %s --norc --suppress 6,7,8" % (v_mis, pslots) - elif alignment_method=="unique": - x = "-v %s -m 1 -p %s --suppress 6,7,8" % (v_mis, pslots) - elif alignment_method=="multiple": - x = "-v %s -M 1 --best --strata -p %s --suppress 6,7,8" % (v_mis, pslots) - elif alignment_method=="k_option": + +def bowtieCommandLiner(alignment_method="RNA", v_mis="1", out_type="tabular", + aligned="None", unaligned="None", input_format="fasta", input="path", + index="path", output="path", pslots="4"): + if input_format == "fasta": + input_format = "-f" + elif input_format == "fastq": + input_format = "-q" + else: + raise Exception('input format must be one of fasta or fastq') + if alignment_method == "RNA": + x = "-v %s -M 1 --best --strata -p %s --norc --suppress 6,7,8" % ( + v_mis, pslots) + elif alignment_method == "unique": + x = "-v %s -m 1 -p %s --suppress 6,7,8" % (v_mis, pslots) + elif alignment_method == "multiple": + x = "-v %s -M 1 --best --strata -p %s --suppress 6,7,8" % ( + v_mis, pslots) + elif alignment_method == "k_option": x = "-v %s -k 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots) - elif alignment_method=="n_option": + elif alignment_method == "n_option": x = "-n %s -M 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots) - elif alignment_method=="a_option": + elif alignment_method == "a_option": x = "-v %s -a --best -p %s --suppress 6,7,8" % (v_mis, pslots) - if aligned == "None" and unaligned == "None": fasta_command = "" - elif aligned != "None" and unaligned == "None": fasta_command= " --al %s" % aligned - elif aligned == "None" and unaligned != "None": fasta_command = " --un %s" % unaligned - else: fasta_command = " --al %s --un %s" % (aligned, unaligned) + if aligned == "None" and unaligned == "None": + fasta_command = "" + elif aligned != "None" and unaligned == "None": + fasta_command = " --al %s" % aligned + elif aligned == "None" and unaligned != "None": + fasta_command = " --un %s" % unaligned + else: + fasta_command = " --al %s --un %s" % (aligned, unaligned) x = x + fasta_command if out_type == "tabular": - return "bowtie %s %s -f %s > %s" % (x, index, input, output) - elif out_type=="sam": - return "bowtie %s -S %s -f %s > %s" % (x, index, input, output) - elif out_type=="bam": - return "bowtie %s -S %s -f %s |samtools view -bS - > %s" % (x, index, input, output) + return "bowtie %s %s %s %s > %s" % (x, index, input_format, input, output) + elif out_type == "sam": + return "bowtie %s -S %s %s %s > %s" % (x, index, input_format, input, output) + elif out_type == "bam": + return "bowtie %s -S %s %s %s |samtools view -bS - > %s" % ( + x, index, input_format, input, output) + def bowtie_squash(fasta): - tmp_index_dir = tempfile.mkdtemp() # make temp directory for bowtie indexes - ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) - ref_file_name = ref_file.name - ref_file.close() # by default, delete the temporary file, but ref_file.name is now stored in ref_file_name - os.symlink( fasta, ref_file_name ) # symlink between the fasta source file and the deleted ref_file name - cmd1 = 'bowtie-build -f %s %s' % (ref_file_name, ref_file_name ) # bowtie command line, which will work after changing dir (cwd=tmp_index_dir) - try: - FNULL = open(os.devnull, 'w') - tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name # a path string for a temp file in tmp_index_dir. Just a string - tmp_stderr = open( tmp, 'wb' ) # creates and open a file handler pointing to the temp file - proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=FNULL, stdout=FNULL ) # both stderr and stdout of bowtie-build are redirected in dev/null - returncode = proc.wait() - tmp_stderr.close() - FNULL.close() - sys.stdout.write(cmd1 + "\n") - except Exception, 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 ) ) - # no Cleaning if no Exception, tmp_index_dir has to be cleaned after bowtie_alignment() - index_full_path = os.path.join(tmp_index_dir, ref_file_name) # bowtie fashion path without extention - return tmp_index_dir, index_full_path - + # make temp directory for bowtie indexes + tmp_index_dir = tempfile.mkdtemp() + ref_file = tempfile.NamedTemporaryFile(dir=tmp_index_dir) + ref_file_name = ref_file.name + # by default, delete the temporary file, but ref_file.name is now stored + # in ref_file_name + ref_file.close() + # symlink between the fasta source file and the deleted ref_file name + os.symlink(fasta, ref_file_name) + # bowtie command line, which will work after changing dir + # (cwd=tmp_index_dir) + cmd1 = 'bowtie-build -f %s %s' % (ref_file_name, ref_file_name) + try: + FNULL = open(os.devnull, 'w') + # a path string for a temp file in tmp_index_dir. Just a string + tmp = tempfile.NamedTemporaryFile(dir=tmp_index_dir).name + # creates and open a file handler pointing to the temp file + tmp_stderr = open(tmp, 'wb') + # both stderr and stdout of bowtie-build are redirected in dev/null + proc = subprocess.Popen( + args=cmd1, shell=True, cwd=tmp_index_dir, stderr=FNULL, stdout=FNULL) + returncode = proc.wait() + tmp_stderr.close() + FNULL.close() + sys.stdout.write(cmd1 + "\n") + 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)) + # no Cleaning if no Exception, tmp_index_dir has to be cleaned after + # bowtie_alignment() + # bowtie fashion path without extention + index_full_path = os.path.join(tmp_index_dir, ref_file_name) + return tmp_index_dir, index_full_path + + def bowtie_alignment(command_line, flyPreIndexed=''): - # make temp directory just for stderr - tmp_index_dir = tempfile.mkdtemp() - tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name - tmp_stderr = open( tmp, 'wb' ) - # conditional statement for sorted bam generation viewable in Trackster - if "samtools" in command_line: - target_file = command_line.split()[-1] # recover the final output file name - path_to_unsortedBam = os.path.join(tmp_index_dir, "unsorted.bam") - path_to_sortedBam = os.path.join(tmp_index_dir, "unsorted.bam.sorted") - first_command_line = " ".join(command_line.split()[:-3]) + " -o " + path_to_unsortedBam + " - " - # example: bowtie -v 0 -M 1 --best --strata -p 12 --suppress 6,7,8 -S /home/galaxy/galaxy-dist/bowtie/Dmel/dmel-all-chromosome-r5.49 -f /home/galaxy/galaxy-dist/database/files/003/dataset_3460.dat |samtools view -bS -o /tmp/tmp_PgMT0/unsorted.bam - - second_command_line = "samtools sort %s %s" % (path_to_unsortedBam, path_to_sortedBam) # generates an "unsorted.bam.sorted.bam file", NOT an "unsorted.bam.sorted" file - p = subprocess.Popen(args=first_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno()) # fileno() method return the file descriptor number of tmp_stderr - returncode = p.wait() - sys.stdout.write("%s\n" % first_command_line + str(returncode)) - p = subprocess.Popen(args=second_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno()) - returncode = p.wait() - sys.stdout.write("\n%s\n" % second_command_line + str(returncode)) - if os.path.isfile(path_to_sortedBam + ".bam"): - shutil.copy2(path_to_sortedBam + ".bam", target_file) - else: - p = subprocess.Popen(args=command_line, shell=True, stderr=tmp_stderr.fileno()) - returncode = p.wait() - sys.stdout.write(command_line + "\n") - tmp_stderr.close() - ## cleaning if the index was created in the fly - if os.path.exists( flyPreIndexed ): - shutil.rmtree( flyPreIndexed ) - # cleaning tmp files and directories - if os.path.exists( tmp_index_dir ): - shutil.rmtree( tmp_index_dir ) - return + # make temp directory just for stderr + tmp_index_dir = tempfile.mkdtemp() + tmp = tempfile.NamedTemporaryFile(dir=tmp_index_dir).name + tmp_stderr = open(tmp, 'wb') + # conditional statement for sorted bam generation viewable in Trackster + if "samtools" in command_line: + # recover the final output file name + target_file = command_line.split()[-1] + path_to_unsortedBam = os.path.join(tmp_index_dir, "unsorted.bam") + path_to_sortedBam = os.path.join(tmp_index_dir, "unsorted.bam.sorted") + first_command_line = " ".join( + command_line.split()[:-3]) + " -o " + path_to_unsortedBam + " - " + # example: bowtie -v 0 -M 1 --best --strata -p 12 --suppress 6,7,8 -S + # /home/galaxy/galaxy-dist/bowtie/Dmel/dmel-all-chromosome-r5.49 -f + # /home/galaxy/galaxy-dist/database/files/003/dataset_3460.dat + # |samtools view -bS -o /tmp/tmp_PgMT0/unsorted.bam - + # generates an "unsorted.bam.sorted.bam file", NOT an + # "unsorted.bam.sorted" file + second_command_line = "samtools sort %s %s" % ( + path_to_unsortedBam, path_to_sortedBam) + # fileno() method return the file descriptor number of tmp_stderr + p = subprocess.Popen( + args=first_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno()) + returncode = p.wait() + sys.stdout.write("%s\n" % first_command_line + str(returncode)) + p = subprocess.Popen( + args=second_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno()) + returncode = p.wait() + sys.stdout.write("\n%s\n" % second_command_line + str(returncode)) + if os.path.isfile(path_to_sortedBam + ".bam"): + shutil.copy2(path_to_sortedBam + ".bam", target_file) + else: + p = subprocess.Popen( + args=command_line, shell=True, stderr=tmp_stderr.fileno()) + returncode = p.wait() + sys.stdout.write(command_line + "\n") + tmp_stderr.close() + # cleaning if the index was created in the fly + if os.path.exists(flyPreIndexed): + shutil.rmtree(flyPreIndexed) + # cleaning tmp files and directories + if os.path.exists(tmp_index_dir): + shutil.rmtree(tmp_index_dir) + return + def __main__(): - args = Parser() - F = open (args.output, "w") - if args.index_from == "history": - tmp_dir, index_path = bowtie_squash(args.index_source) - else: - tmp_dir, index_path = "dummy/dymmy", args.index_source - command_line = bowtieCommandLiner(args.method, args.v_mismatches, args.output_format, args.aligned, args.unaligned, args.input, index_path, args.output, args.num_threads) - bowtie_alignment(command_line, flyPreIndexed=tmp_dir) - F.close() -if __name__=="__main__": __main__() + args = Parser() + F = open(args.output, "w") + if args.index_from == "history": + tmp_dir, index_path = bowtie_squash(args.index_source) + else: + tmp_dir, index_path = "dummy/dymmy", args.index_source + command_line = bowtieCommandLiner(args.method, args.v_mismatches, args.output_format, + args.aligned, args.unaligned, args.input_format, args.input, + index_path, args.output, args.num_threads) + bowtie_alignment(command_line, flyPreIndexed=tmp_dir) + F.close() +if __name__ == "__main__": + __main__() diff -r 64064dccdb11 -r b50d7228b678 sRbowtie.xml --- a/sRbowtie.xml Mon Nov 03 10:24:38 2014 -0500 +++ b/sRbowtie.xml Sun Mar 29 10:25:36 2015 -0400 @@ -1,11 +1,11 @@ - for FASTA small reads - - bowtie + for FASTA small reads + + bowtie samtools - - - sRbowtie.py --input $input + + sRbowtie.py --input $input + --input-format $input.extension --method $method --v-mismatches $v_mismatches --output-format $output_format @@ -22,101 +22,102 @@ --unaligned $unaligned --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - additional_fasta == "al" or additional_fasta == "al_and_unal" - - - additional_fasta == "unal" or additional_fasta == "al_and_unal" - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + additional_fasta == "al" or additional_fasta == "al_and_unal" + + + additional_fasta == "unal" or additional_fasta == "al_and_unal" + + + + + + + + + + + + + + + + + + + + + + + **What it does** @@ -209,4 +210,7 @@ **Matched and unmatched fasta reads can be retrieved, for further analyses** + + 10.1186/gb-2009-10-3-r25 + diff -r 64064dccdb11 -r b50d7228b678 test-data/297_reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/297_reference.fa Sun Mar 29 10:25:36 2015 -0400 @@ -0,0 +1,118 @@ +>FBgn0000005_297 +AGTGACGTATTTGGGTGGTCCAAACCAGCCACTTCCATTATTTCAAAGAAATCAGTAATG +CACTCTAGTAATTTTCCATAACTGTATCCCAGCTGCGCAGACTCGTTTATCTTTTGCAGC +GCAGCGTTCTTTGTAAACATCCTAAAGACCTGCCTAAGCAGATTTGACTGCCCTCTTTCA +ACGCTACCTAATCTTAAGAACCCAAGAGCGAGGCTCTCCCGAAATACAAATATTGTTCAA +ATACTGAGGCTTCTCCTCAATCCAATTTGCATTTGATTTTTAGTCTTAAGCTGAGATCCA +AAGAATAAAGTCGTGAAACTATTTCTCCTAAAAACTATTTTTTATTTCTTGGCGTTGTCC +TTAGTCAACTGACGGGACATTAGTTCGACTCATAAATAAAACAACAATTTTACTGGCGCA +GTCGGTAGGATACAAAAGTATCCGAAAAAAAAGAACCTTCGAATGGAAAATAAGTTAAAT +TTTATAGTCCTGTGCTCGAAACATCTCCCAAAATAAATTCGTGAAAACTCTTCAACTTCA +ATTATAATTCCAATTCGGTTATCCAATAATAAGTGGAAGTGAAATACGAAACAAAAATAT +TAAGTCCAAAGGCAACTAAGTTTTAAAACCAACATATAAAAATAAAAAATTAAAACAATA +TAGAATTTTAATAATACAACACAAAAATTTACAAAACAAAAAAACAAACAAGTGAAACTA +GAAAGCTTAAAAATAATAATAACATTGAATCCGAAACAAAACAAAAAAATAAAACACAAA +AGTTAAAAATTTTACAATAAAAATGTCACAACCAATTATTGCGCTGAGCGACATAAACCT +TGCCGAAGCCCGTCGGCAGCTTAAAGACATTATGCCATTCAAGGGTGATCCAGAAACCCT +TCACACCTTTATCAGCAGAGTGGATTACGTAATTTCGCTCTACCAAACAAATGATGTCCG +ACAACAGAGGATTCTACTGGGAGCCATCGAAAGGAACTTGGACGGACAAATTACACGATC +TTTGGGACTTCCGAACGTCGAAGATTGGCCTACCCTTAAAGCAAGACTCATCGCGGAATT +TAAAATTCAAACACCAAACTACAAACTTCTGGAGAACTTCAGGGAGACACCATACAGAGG +AAGCCTAAGAGCATTCTGCGAAGAAGCGGAGAGACGACGTCAATTACTAATTTCGAAACT +ACACCTGGAAGGTAACCAATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT +TAAGATACTGATAAGGAAACTACCAATACAATTATTCACTATTTTAGCCCATCACGATAT +TACAGACTTAAGATCCTTAATTACCATTGCACAAAATGAGGGAATTTATGAAGAACACAT +TAATTTTGAATTTTATGAAAAACCAGAATATCGTAATAAAAATTCAAATTCTAACCAGAA +TTCGAAAACACAAAAATTCAATACAAATGTTCAAACTCAAAATCGACCAAGTTACTCACA +ATATTCCCAACCCTTCCAACCTAATTTTAATCAATACATTCAACCATTTAGACCTAGCTA +TACACAGCAGATAACTAACAACCCACCCATGTGGCACGCACCTAATTATTTCAGACCCAA +CCAATACATAAACCCACAACCCATTATTCAAAAAAATCATTTCCAACAATATCCCAACAA +AGCCCAATTTCCCCAAACAACGCATTTTAGAGGAAATACATACCCTCGACTACAACAACC +CTCTACATATAAAAATACTAACTTCCCGATTACTAAACGACTAAGACCATCGGACAGTGA +ACAAACTAAAATGTCTATTGACGAAATTAGATTCCAAGACGCGCATGAATTCGAACAAGT +CCAACCTAATTATTACGAGCAACAGTATTTTAACCAAAATCAATACAATCCGTATCAAAA +TCATAGCTTCATTAATGAAGGGCAACAACAAGTTCAATTTGTACAAATTAATAACAAACA +AAACCAAAATAATTCTGAACTAAACGAAAATTTTCGGTTAACAGTTCCGGAAAATACGAA +TACATAAAAATAGTATACAAAGGGCGTTCATACAAATGCCTTCTAGACACAGGATCAACA +ATTAATATGATCAATGAAAATATATTTTGTCTTCCCATTCAAAATAGTAGATGTGAAGTT +TTAACATCAAATGGCCCTATTACCTTGAACGACTTGATTATGTTACCCAGAAATAGTATT +TTCAAAAAAACCGAACCATTTTATGTGCACAGATTTTCTAATAATTACGATATGCTAATT +GGCAGAAAATTGTTGAAAAATGCTCAATCAGTTATTAATTACAAAAATGATACAGTTACC +CTTTTTGATCAAACATACAAATTAATTACTTCAGAATCCGAAAGAAACCAAAATTTGTAT +ATCCAAAGGACACCAGAATCAATTGCAAGCTCAGATCAGGAATCAATAAAAAAATTAGAT +TTTTCACAGTTTCGATTAGATCACCTAAATCAGGAGGAAACTTTTAAGTTAAAAGGCTTG +TTAAATAAATTTAGAAATCTTGAATATAAGGAGGGAGAGAAATTAACATTTACAAATACA +ATTAAACACGTACTAAATACAACACATAACTCCCCAATTTATTCGAAACAATACCCACTT +GCGCAAACACACGAAATCGAAGTAGAAAACCAAGTACAGGAAATGCTGAATCAGGGATTA +ATTAGGGAAAGTAATTCTCCATACAATAGTCCTACTTGGGTCGTACCAAAGAAACCGGAT +GCTTCTGGTGCAAATAAGTACAGGGTAGTAATTGATTATAGAAAGCTAAATGAAATAACC +ATACCTGACAGATATCCAATTCCAAATATGGACGAAATTCTTGGCAAACTGGGTAAATGC +CAATATTTTACAACGATCGATCTGGCAAAGGGATTTCATCAAATAGAAATGGACGAAGAA +TCAATTTCTAAAACTGCATTCTCCACAAAAAGCGGTCATTACGAATACCTTCGAATGCCA +TTTGGCCTTAGGAATGCACCCGCTACTTTTCAAAGGTGCATGAATAATATCCTTCGACCG +TTGCTTAACAAACACTGTTTGGTGTATCTGGATGATATTATAATTTTTTCAACATCCCTT +ACAGAACATTTAAATTCAATACAATTAGTTTTTACAAAGCTTGCAGATGCAAATTTAAAA +TTGCAACTAGACAAATGTGAGTTCTTAAAAAAGGAAGCTAACTTTCTTGGTCACATAGTT +ACCCCTGATGGTATTAAACCAAATCCTATTAAAGTTAAAGCCATAGTTTCATACCCAATT +CCGACAAAAGATAAAGAGATAAGAGCTTTCCTTGGATTAACAGGTTATTATCGCAAATTT +ATTCCAAATTACGCAGACATAGCAAAACCCATGACCAGCTGCTTAAAAAAAAGGACAAAG +ATAGATACACAAAAACTTGAGTACATAGAGGCATTCGAAAAACTTAAGGCTTTGATAATT +CGTGACCCAATTTTACAATTACCTGATTTTGAAAAGAAATTTGTTTTAACCACAGATGCA +AGTAACTTGGCCCTCGGGGCTGTCCTTTCTCAAAACGGTCATCCTATATCTTTTATTAGT +AGAACACTTAACGATCACGAATTAAATTACAGTGCTATCGAAAAAGAATTACTTGCCATA +GTTTGGGCCACAAAAACTTTTCGACATTATTTACTAGGACGACAATTTCTCATTGCCAGT +GACCATCAACCTCTTAGATGGCTTCATAACTTAAAGGAACCAGGTGCTAAGTTAGAAAGA +TGGAGAGTTAGATTAAGCGAATACCAATTTAAAATAGATTATATTAAAGGGAAAGAAAAT +TCAGTTGCCGATGCATTATCAAGAATTAAAATTGAAGAAAATCATCATAGTGAAGCTACT +CAACATAGTGCAGAAGAGGACAATAGCAACCTTATTCATTTAACAGAAAAACCAATAAAT +TATTTCAAAAAACAAATAATCTTTATTAAATCCGATAAAAATAAAGTAGAGCATTCAAAA +ATATTCGGTAACTCCATTACCACAATTCAATATGACGTAATGACACTTGAAAAGGCCAAA +CAAATTTTACTCGATCACTTTATCCATAGAAACATTACCATTTATATTGAGAGCGATGTA +GATTTTGAAATCGTTCAAAGAGCACACATAGAAATTGTTAATACCACCTACACAAAAGTA +ATTCGCAGTCTTTTCCTATTAAAGAACGTTGGTTCATACGCCGAATTCAAAGAAATCATA +CTTCAATCACATGAAAAACTTTTACACCCTGGTATACAGAAAATGACAAAATTATTTAAA +GAAAATCACTTCTTTCCAAATAGCCAACTATTAATTCAGAATATAATAAACGAATGCAAC +ATATGCAATTTGGCCAAAACAGAACATAGAAACACCAAAATGCCTTTAAAAATCACACCC +AACCCGGAACATTGCCGAGAAAAATTTGTAGTAGATATTTATTCATCTGAGGGAAAACAT +TACATCAGTTGCATTGATATTTATTCTAAATTCGCTACACTTGAGCAAATTAAAACTAAG +GATTGGATAGAATGCAGAAACGCATTAATGCGCATTTTTAATCAACTAGGAAAACCCAAA +TTATTAAAGGCAGACAGAGACGGAGCTTTCTCCAGTTTAGCTTTAAAGCGATGGCTTGAA +GAAGAAGAAGTCGAATTACAGCTCAATACAGCAAAAAACGGAGTAGCAGACGTCGAAAGA +TTACACAAAACAATAAATGAAAAAATTCGTATAATCAATTCATCTGATGATGAAGAAGTA +AAATTAAGCAAGATAGAAACAATCCTCTACACATACAACCAAAAAATTAAACATGACACT +ACTGGACAGAGACCTGCTCAAATTTTCTTATACGCTGGGCATCCCATATTAGACACTCAA +AAAATTAAAGAGAAGAAAATAGAGAAAATAAATGAAGACAGACGGGAATTTAATATTGAC +ACTAATTACAGAAAAGGTCCACTACAGAAAGGCAAATTAGAAAACCCATTTAAACCAACC +AAAAATGTAGAACAGACAGACCCTGACCATTACAAAATCACTAATAGAAATAGAGTTACG +CACTACTACAAAACACAATTCAAAAAACAAAAGAAAAATAATAAACTCTCAATTTCACAG +GCACCTGGTACCCGATAACACTATTGTTTATACTGATCACAGCTGTTCATGGACAACAAA +TTCAAATTAATAATATTGACACCAACCACGGATATCTCCTTTTTTCTGATAAGCCAGTAC +AGATACCATCCTCCTTTGAACATCACTCCTTAAAAATCAATTTAACTGAAATAGACATCG +TGGTTGACTATTTTGAGCAAAGACTACGAACCGATTACCATGCACCCCAGATCAATTTTT +TATACAATAAAATAAAAAGAGAACTAGCCAGAATAACCCTGAAACATAGAAACAAACGGG +GTTTTATTAACATTGTGGGTTCAGGTTTTAAATACCTATTTGGAACACTAGATGAAAATG +ATCGAGTCGAAATACAGAAAAAACTTGAAATCAACGTCCATAACTCAGTAAAATTACATG +AACTCAACGACGCCATACGATTGATAAATGACGGAATGCAAAAAATACAGAATTATGAAA +ATAACCACACCATCATTGACAGTCTTTTGTTCGAACTAATGCAGTTTACGGAATACATAG +AAGATTTGGAAATGGCTATGCAGCTTTCCAGACTTGGACTGTTTAACCCCAAATTACTAA +ACTACGACAAACTTGAAAATGTGAACAGCCAAAACATTTTGAACATTAAAACATCCACTT +GGATTAACTACAATGATAACCAAGTATTAATCATATCCCACATACCCATTTACCTTTCAC +TAATAAGCACAATTAAAATAATTCCTTACCCAGACTCCAACGGCTATCAGCTAGATTACA +CAGACACACAATCATATTTTGAAAAAGAAAATAAAGTTTATAATACCGAAAATAAAGAAG +TAAAAAATGAATGTGTCACCAATATTATTAAACACTTAAATCCAATTTGTAATTTTAAGC +CAGTACACACGAACGAAATAATAAAATACATAGAACCAAACACAATTGTAACTTGGAACT +TAACCCAAACAATTCTTAACCAAAATTGCCAAAATTCAATTAATAAAATAAAAATAGAAG +GAAACAAAATGATAAGAGTAACGCAATGCAAAATAGAAATCAATAATATAAATTTTAGTG +AAACTCTGTTAGAACCAGAAATAGATTTGACACCACTATACACACCACTTAATATAACAA +AAATAAAAATTGTAAAACACAACGACATTATTGAGATGATTTCAGAGAACAATATTACAC +TTTACATACAAATGATCATTGTAATAATCGCACTAATTTTGTTGTACTCATATTTAAGAT +ATGTATCATTTAAACCATTTATGATGTTGTATGCAAAACTTAAAATAAGAAAAAATCAAA +ATCAAAACACACCACAACAAACAGAAATAGAAGAAATTCCATTTCCCACACTATATCCAT +CAATCCCAGCCCAAGTATAGGCTTCTCTTTAAGGGAAGGGGAGTGACGTATTTGGGTGGT +CCAAACCAGCCACTTCCATTATTTCAAAGAAATCAGTAATGCACTCTAGTAATTTTCCAT +AACTGTATCCCAGCTGCGCAGACTCGTTTATCTTTTGCAGCGCAGCGTTCTTTGTAAACA +TCCTAAAGACCTGCCTAAGCAGATTTGACTGCCCTCTTTCAACGCTACCTAATCTTAAGA +ACCCAAGAGCGAGGCTCTCCCGAAATACAAATATTGTTCAAATACTGAGGCTTCTCCTCA +ATCCAATTTGCATTTGATTTTTAGTCTTAAGCTGAGATCCAAAGAATAAAGTCGTGAAAC +TATTTCTCCTAAAAACTATTTTTTATTTCTTGGCGTTGTCCTTAGTCAACTGACGGGACA +TTAGTTCGACTCATAAATAAAACAACAATTTTACT diff -r 64064dccdb11 -r b50d7228b678 test-data/input.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fa Sun Mar 29 10:25:36 2015 -0400 @@ -0,0 +1,10 @@ +>1 +CATTCTGCGAAGAAGC +>2 +GGAGAGACGACGTCAATTACT +>3 +AATTTCGAAACTACACCTGGAAGGTAACCA +>4 +ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT +>5 +TAAGATACTGATAAGGAAACTACCAATA diff -r 64064dccdb11 -r b50d7228b678 test-data/input.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fastq Sun Mar 29 10:25:36 2015 -0400 @@ -0,0 +1,20 @@ +@HTW-1 +CATTCTGCGAAGAAGC ++ +HHHHHHHHHHHHHHHH +@HTW-2 +GGAGAGACGACGTCAATTACT ++ +HHHHHHHHHHHHHHHHHHHHH +@HTW-3 +AATTTCGAAACTACACCTGGAAGGTAACCA ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH +@HTW-4 +ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH +@HTW-5 +TAAGATACTGATAAGGAAACTACCAATA ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHH diff -r 64064dccdb11 -r b50d7228b678 test-data/output.bam Binary file test-data/output.bam has changed diff -r 64064dccdb11 -r b50d7228b678 test-data/output2.bam Binary file test-data/output2.bam has changed diff -r 64064dccdb11 -r b50d7228b678 test-data/sRbowtie.fa --- a/test-data/sRbowtie.fa Mon Nov 03 10:24:38 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ ->1 -GTATTGTAAGTGGCAGAGTGGC ->2 -TGGAATGTAAAGAAGTATGGAG ->3 -GTGGGGAGTTTGGATGGGGCGGCA ->4 -AATGGCACTGGAAGAATTCACGG ->5 -GTACGGACAAGGGGAATC ->6 -TTGGGTTCTGGGGGGAGTATGG ->7 -GTGGGGAGTTTCGCTGGGGCGGCA ->8 -TAAGGGTCGGGTAGTGAGGGC ->9 -AGCTGGGACTGAGGACTG ->10 -AGCTGGGACTGAGGACTGC ->11 -AAGGGTCGGGTAGTGAGG ->12 -GTCGGGTAGTGAGGGCCTT ->13 -TGGTGGGGCTTGGAACAATTGGAGGGC ->14 -TGACGGAAGGGCACCACC ->15 -TGGAATGTAAAGAAGTATGGAG ->16 -TTGGGTTCTGGGGGGAGT ->17 -TCAGGTGGGGAGTTTGGCTGGGGCGGCACA ->18 -TTGGGTATAGGGGCGAAAGA ->19 -AGCGGGCGTGCTTGTGGAC ->20 -GTCGAATTTGGGTATAGGGGC diff -r 64064dccdb11 -r b50d7228b678 test-data/sRbowtie.out --- a/test-data/sRbowtie.out Mon Nov 03 10:24:38 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -2 + 2L 20487495 TGGAATGTAAAGAAGTATGGAG -4 - 2L 11953463 CCGTGAATTCTTCCAGTGCCATT -15 + 2L 20487495 TGGAATGTAAAGAAGTATGGAG -14 - Uextra 7115665 GGTGGTGCCCTTCCGTCA -18 + Uextra 7726410 TTGGGTATAGGGGCGAAAGA diff -r 64064dccdb11 -r b50d7228b678 tool_dependencies.xml --- a/tool_dependencies.xml Mon Nov 03 10:24:38 2014 -0500 +++ b/tool_dependencies.xml Sun Mar 29 10:25:36 2015 -0400 @@ -1,7 +1,7 @@ - +