Mercurial > repos > devteam > bowtie_wrappers
changeset 4:bdd9fcdb398e draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 397bc85634156862fdaa3d74b8f1e53752876619
| author | devteam |
|---|---|
| date | Thu, 04 May 2017 14:59:41 -0400 |
| parents | 9326d6e6882a |
| children | cc439755faab |
| files | bowtie_wrapper.py bowtie_wrapper.xml |
| diffstat | 2 files changed, 56 insertions(+), 56 deletions(-) [+] |
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--- a/bowtie_wrapper.py Sun Jan 08 08:00:56 2017 -0500 +++ b/bowtie_wrapper.py Thu May 04 14:59:41 2017 -0400 @@ -64,19 +64,24 @@ --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is' """ -import optparse, os, shutil, subprocess, sys, tempfile +import optparse +import os +import shutil +import subprocess +import sys +import tempfile -#Allow more than Sanger encoded variants +# 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 +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.stderr.write( '%s\n' % msg ) - sys.exit() + sys.exit('%s\n' % msg) + def __main__(): - #Parse Command Line 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' ) @@ -152,7 +157,7 @@ # index if necessary if options.genomeSource == 'history' and not options.do_not_build_index: # set up commands - if options.index_settings =='indexPreSet': + if options.index_settings == 'indexPreSet': indexing_cmds = '%s' % colorspace else: try: @@ -204,7 +209,7 @@ ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc, inoref, options.ioffrate, iftab, intoa, iendian, iseed, colorspace ) - except ValueError, e: + except ValueError as e: # clean up temp dir if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) @@ -216,25 +221,22 @@ cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name ) try: tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name - tmp_stderr = open( tmp, 'wb' ) - proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp, 'rb' ) - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() + 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: - raise Exception, stderr - except Exception, e: + # 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 ) @@ -261,7 +263,7 @@ 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 ) + ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding ) else: try: if options.skip and int( options.skip ) > 0: @@ -280,13 +282,13 @@ 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'): + 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'): + 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 = '' @@ -400,7 +402,7 @@ strata, offrate, seed, snpphred, snpfrac, keepends, output_unmapped_reads, output_suppressed_reads, quality_score_encoding ) - except ValueError, e: + except ValueError as e: # clean up temp dir if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) @@ -415,51 +417,48 @@ cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output ) # align tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name - tmp_stderr = open( tmp, 'wb' ) - proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stdout=sys.stdout, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() + 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 - tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() + 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 + 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: + options.output_suppressed_reads_l and options.output_suppressed_reads_r: try: left = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' ) right = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' ) shutil.move( left, options.output_suppressed_reads_l ) shutil.move( right, options.output_suppressed_reads_r ) - except Exception, e: + 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: + options.output_unmapped_reads_l and options.output_unmapped_reads_r: try: left = tmp_unmapped_file_name.replace( '.fastq', '_1.fastq' ) right = tmp_unmapped_file_name.replace( '.fastq', '_2.fastq' ) shutil.move( left, options.output_unmapped_reads_l ) shutil.move( right, options.output_unmapped_reads_r ) - except Exception, e: + 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, e: + 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 @@ -468,5 +467,6 @@ stdout += 'Sequence file aligned.\n' sys.stdout.write( stdout ) + if __name__ == "__main__": __main__()
--- a/bowtie_wrapper.xml Sun Jan 08 08:00:56 2017 -0500 +++ b/bowtie_wrapper.xml Thu May 04 14:59:41 2017 -0400 @@ -1,8 +1,8 @@ <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.2.0"> + <description></description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> </requirements> - <description></description> <version_command>bowtie --version</version_command> <command> python '$__tool_directory__/bowtie_wrapper.py' @@ -167,7 +167,7 @@ </param> </when> <when value="history"> - <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" /> + <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" /> <conditional name="indexParams"> <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index"> <option value="indexPreSet">Default</option> @@ -313,7 +313,7 @@ <when value="paired"> <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> - <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">> + <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()"> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>