Mercurial > repos > devteam > data_manager_sam_fasta_index_builder
changeset 5:cc4ef4d38cf9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
author | iuc |
---|---|
date | Mon, 18 Nov 2019 15:07:34 -0500 |
parents | 1865e693d8b2 |
children | f8418a1bf7d0 |
files | data_manager/data_manager_sam_fasta_index_builder.py data_manager/data_manager_sam_fasta_index_builder.xml test-data/all_fasta.loc test-data/fasta_indexes.loc test-data/phiX174.fasta test-data/sam_fasta_data_manager.json tool_data_table_conf.xml.test |
diffstat | 6 files changed, 163 insertions(+), 34 deletions(-) [+] |
line wrap: on
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--- a/data_manager/data_manager_sam_fasta_index_builder.py Thu Sep 14 15:30:56 2017 -0400 +++ b/data_manager/data_manager_sam_fasta_index_builder.py Mon Nov 18 15:07:34 2019 -0500 @@ -13,7 +13,7 @@ DEFAULT_DATA_TABLE_NAME = "fasta_indexes" -def get_id_name( params, dbkey, fasta_description=None): +def get_id_name(params, dbkey, fasta_description=None): # TODO: ensure sequence_id is unique and does not already appear in location file sequence_id = params['param_dict']['sequence_id'] if not sequence_id: @@ -27,65 +27,73 @@ return sequence_id, sequence_name -def build_sam_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): +def build_sam_index(data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME): # TODO: allow multiple FASTA input files - assert os.path.exists( fasta_filename ), 'FASTA file "%s" is missing, cannot build samtools index.' % fasta_filename - fasta_base_name = os.path.split( fasta_filename )[-1] - sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) - os.symlink( fasta_filename, sym_linked_fasta_filename ) + assert os.path.exists(fasta_filename), 'FASTA file "%s" is missing, cannot build samtools index.' % fasta_filename + fasta_base_name = os.path.split(fasta_filename)[-1] + sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name) + os.symlink(fasta_filename, sym_linked_fasta_filename) - args = [ 'samtools', 'faidx' ] - args.append( sym_linked_fasta_filename ) + args = ['samtools', 'faidx'] + args.append(sym_linked_fasta_filename) tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-sam_fa_index_builder-stderr") - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) + proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno()) return_code = proc.wait() if return_code: tmp_stderr.flush() - tmp_stderr.seek( 0 ) - sys.stderr.write( "Error building index:\n" ) + tmp_stderr.seek(0) + sys.stderr.write("Error building index:\n") while True: - chunk = tmp_stderr.read( CHUNK_SIZE ) + chunk = tmp_stderr.read(CHUNK_SIZE) if not chunk: break - sys.stderr.write( chunk ) - sys.exit( return_code ) + sys.stderr.write(chunk) + sys.exit(return_code) tmp_stderr.close() - data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) - _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) + data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name) + _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) -def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): - data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) - data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) - data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) +def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry): + data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) + data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, []) + data_manager_dict['data_tables'][data_table_name].append(data_table_entry) return data_manager_dict def main(): parser = optparse.OptionParser() - parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) - parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) - parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) - parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) + parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename') + parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey') + parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description') + parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name') (options, args) = parser.parse_args() filename = args[0] - params = json.loads( open( filename ).read() ) - target_directory = params[ 'output_data' ][0]['extra_files_path'] - os.mkdir( target_directory ) + params = json.loads(open(filename).read()) + target_directory = params['output_data'][0]['extra_files_path'] + os.mkdir(target_directory) data_manager_dict = {} - if options.fasta_dbkey in [ None, '', '?' ]: - raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) + if options.fasta_dbkey in [None, '', '?']: + raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (options.fasta_dbkey)) - sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) + sequence_id, sequence_name = get_id_name(params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description) # build the index - build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME ) + build_sam_index( + data_manager_dict, + options.fasta_filename, + target_directory, + options.fasta_dbkey, + sequence_id, + sequence_name, + data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME + ) # save info to json file - open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) + open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True)) if __name__ == "__main__":
--- a/data_manager/data_manager_sam_fasta_index_builder.xml Thu Sep 14 15:30:56 2017 -0400 +++ b/data_manager/data_manager_sam_fasta_index_builder.xml Mon Nov 18 15:07:34 2019 -0500 @@ -1,7 +1,7 @@ -<tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.2"> +<tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.3" profile="19.05"> <description>builder</description> <requirements> - <requirement type="package" version="1.5">samtools</requirement> + <requirement type="package" version="1.9">samtools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/data_manager_sam_fasta_index_builder.py' @@ -21,6 +21,12 @@ <outputs> <data name="out_file" format="data_manager_json"/> </outputs> + <tests> + <test> + <param name="all_fasta_source" value="phiX174"/> + <output name="out_file" value="sam_fasta_data_manager.json"/>" + </test> + </tests> <help> .. class:: infomark
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Mon Nov 18 15:07:34 2019 -0500 @@ -0,0 +1,19 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# +phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.fasta Mon Nov 18 15:07:34 2019 -0500 @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sam_fasta_data_manager.json Mon Nov 18 15:07:34 2019 -0500 @@ -0,0 +1,1 @@ +{"data_tables": {"fasta_indexes": [{"dbkey": "phiX174", "name": "phiX174", "path": "phiX174.fasta", "value": "phiX174"}]}} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Nov 18 15:07:34 2019 -0500 @@ -0,0 +1,16 @@ +<tables> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> + <!-- + <table name="__dbkeys__" comment_char="#"> + <columns>value, name, len_path</columns> + <file path="${__HERE__}/test-data/dbkeys.loc" /> + </table> + --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables>