Mercurial > repos > devteam > data_manager_gatk_picard_index_builder
changeset 4:6287d0ee459e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gatk_picard_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
| author | iuc |
|---|---|
| date | Sun, 22 Nov 2020 12:49:20 +0000 |
| parents | b31f1fcb203c |
| children | e6ff5470023c |
| files | data_manager/data_manager_gatk_picard_index_builder.py tool_dependencies.xml |
| diffstat | 2 files changed, 95 insertions(+), 98 deletions(-) [+] |
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--- a/data_manager/data_manager_gatk_picard_index_builder.py Tue Apr 04 18:08:38 2017 -0400 +++ b/data_manager/data_manager_gatk_picard_index_builder.py Sun Nov 22 12:49:20 2020 +0000 @@ -14,7 +14,7 @@ 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: @@ -28,98 +28,93 @@ return sequence_id, sequence_name -def build_picard_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, jar, data_table_name=DEFAULT_DATA_TABLE_NAME ): - fasta_base_name = os.path.split( fasta_filename )[-1] - gatk_sorted_fasta_filename = os.path.join( target_directory, fasta_base_name ) - shutil.copy( fasta_filename, gatk_sorted_fasta_filename ) - _sort_fasta_gatk( gatk_sorted_fasta_filename ) +def build_picard_index(data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, jar, data_table_name=DEFAULT_DATA_TABLE_NAME): + fasta_base_name = os.path.split(fasta_filename)[-1] + gatk_sorted_fasta_filename = os.path.join(target_directory, fasta_base_name) + shutil.copy(fasta_filename, gatk_sorted_fasta_filename) + _sort_fasta_gatk(gatk_sorted_fasta_filename) sam_index_filename = '%s.fai' % gatk_sorted_fasta_filename - if not os.path.exists( sam_index_filename ): - sam_command = [ 'samtools', 'faidx', gatk_sorted_fasta_filename ] - _run_command( sam_command, target_directory ) - args = [ 'java', '-jar', jar, 'R=%s' % gatk_sorted_fasta_filename, 'O=%s.dict' % sequence_id ] - _run_command( args, target_directory ) - 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 ) + if not os.path.exists(sam_index_filename): + sam_command = ['samtools', 'faidx', gatk_sorted_fasta_filename] + _run_command(sam_command, target_directory) + args = ['java', '-jar', jar, 'R=%s' % gatk_sorted_fasta_filename, 'O=%s.dict' % sequence_id] + _run_command(args, target_directory) + 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 _run_command( command, target_directory ): - tmp_stderr = tempfile.NamedTemporaryFile( prefix="tmp-data-manager-gatk_picard_index_builder-stderr" ) - proc = subprocess.Popen( args=command, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) +def _run_command(command, target_directory): + tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-gatk_picard_index_builder-stderr") + proc = subprocess.Popen(args=command, 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() -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 _move_and_index_fasta_for_sorting( fasta_filename ): +def _move_and_index_fasta_for_sorting(fasta_filename): unsorted_filename = tempfile.NamedTemporaryFile().name - shutil.move( fasta_filename, unsorted_filename ) + shutil.move(fasta_filename, unsorted_filename) fasta_offsets = {} - unsorted_fh = open( unsorted_filename ) - while True: - offset = unsorted_fh.tell() - line = unsorted_fh.readline() - if not line: - break - if line.startswith( ">" ): - line = line.split( None, 1 )[0][1:] - fasta_offsets[ line ] = offset - unsorted_fh.close() - current_order = [x[1] for x in sorted( ( x[1], x[0] ) for x in fasta_offsets.items() )] - return ( unsorted_filename, fasta_offsets, current_order ) + with open(unsorted_filename) as unsorted_fh: + while True: + offset = unsorted_fh.tell() + line = unsorted_fh.readline() + if not line: + break + if line.startswith(">"): + line = line.split(None, 1)[0][1:] + fasta_offsets[line] = offset + current_order = [x[1] for x in sorted((x[1], x[0]) for x in fasta_offsets.items())] + return (unsorted_filename, fasta_offsets, current_order) -def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ): - unsorted_fh = open( unsorted_fasta_filename ) - sorted_fh = open( sorted_fasta_filename, 'wb+' ) - - for name in sorted_names: - offset = fasta_offsets[ name ] - unsorted_fh.seek( offset ) - sorted_fh.write( unsorted_fh.readline() ) - while True: - line = unsorted_fh.readline() - if not line or line.startswith( ">" ): - break - sorted_fh.write( line ) - unsorted_fh.close() - sorted_fh.close() +def _write_sorted_fasta(sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename): + with open(unsorted_fasta_filename, 'rb') as unsorted_fh, open(sorted_fasta_filename, 'wb+') as sorted_fh: + for name in sorted_names: + offset = fasta_offsets[name] + unsorted_fh.seek(offset) + sorted_fh.write(unsorted_fh.readline()) + while True: + line = unsorted_fh.readline() + if not line or line.startswith(b">"): + break + sorted_fh.write(line) -def _int_to_roman( integer ): - if not isinstance( integer, int ): - raise TypeError("expected integer, got %s" % type( integer )) +def _int_to_roman(integer): + if not isinstance(integer, int): + raise TypeError("expected integer, got %s" % type(integer)) if not 0 < integer < 4000: - raise ValueError("Argument must be between 1 and 3999, got %s" % str( integer )) - ints = ( 1000, 900, 500, 400, 100, 90, 50, 40, 10, 9, 5, 4, 1 ) - nums = ( 'M', 'CM', 'D', 'CD', 'C', 'XC', 'L', 'XL', 'X', 'IX', 'V', 'IV', 'I' ) + raise ValueError("Argument must be between 1 and 3999, got %s" % str(integer)) + ints = (1000, 900, 500, 400, 100, 90, 50, 40, 10, 9, 5, 4, 1) + nums = ('M', 'CM', 'D', 'CD', 'C', 'XC', 'L', 'XL', 'X', 'IX', 'V', 'IV', 'I') result = "" - for i in range( len( ints ) ): - count = int( integer / ints[ i ] ) - result += nums[ i ] * count - integer -= ints[ i ] * count + for i in range(len(ints)): + count = int(integer / ints[i]) + result += nums[i] * count + integer -= ints[i] * count return result -def _sort_fasta_gatk( fasta_filename ): - ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename ) - sorted_names = list(map( str, range( 1, 100 ) )) + list(map( _int_to_roman, range( 1, 100 ) )) + [ 'X', 'Y', 'M' ] +def _sort_fasta_gatk(fasta_filename): + (unsorted_filename, fasta_offsets, current_order) = _move_and_index_fasta_for_sorting(fasta_filename) + sorted_names = list(map(str, range(1, 100))) + list(map(_int_to_roman, range(1, 100))) + ['X', 'Y', 'M'] # detect if we have chrN, or just N has_chr = False for chrom in sorted_names: @@ -130,58 +125,60 @@ if has_chr: sorted_names = ["chr%s" % x for x in sorted_names] else: - sorted_names.insert( 0, "MT" ) - sorted_names.extend( "%s_random" % x for x in sorted_names ) + sorted_names.insert(0, "MT") + sorted_names.extend(["%s_random" % x for x in sorted_names]) existing_sorted_names = [] for name in sorted_names: # Append each chromosome only once. if name in current_order and name not in existing_sorted_names: - existing_sorted_names.append( name ) + existing_sorted_names.append(name) for name in current_order: # TODO: confirm that non-canonical names do not need to be sorted specially if name not in existing_sorted_names: - existing_sorted_names.append( name ) + existing_sorted_names.append(name) if existing_sorted_names == current_order: - shutil.move( unsorted_filename, fasta_filename ) + shutil.move(unsorted_filename, fasta_filename) else: - _write_sorted_fasta( existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename ) + _write_sorted_fasta(existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename) 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( '-j', '--jar', dest='jar', action='store', type="string", default=None, help='GATK .jar file' ) + 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('-j', '--jar', dest='jar', action='store', type="string", default=None, help='GATK .jar file') (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 ) + with open(filename) as fh: + params = json.load(fh) + 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_picard_index( data_manager_dict, - options.fasta_filename, - target_directory, - options.fasta_dbkey, - sequence_id, - sequence_name, - options.jar, - data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME ) + build_picard_index(data_manager_dict, + options.fasta_filename, + target_directory, + options.fasta_dbkey, + sequence_id, + sequence_name, + options.jar, + 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 ) ) + with open(filename, 'w') as fh: + json.dump(data_manager_dict, fh, sort_keys=True) if __name__ == "__main__":
--- a/tool_dependencies.xml Tue Apr 04 18:08:38 2017 -0400 +++ b/tool_dependencies.xml Sun Nov 22 12:49:20 2020 +0000 @@ -1,9 +1,9 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <tool_dependency> - <package name="picard" version="1.56.0"> - <repository changeset_revision="99a28567c3a3" name="package_picard_1_56_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="picard" version="1.56.0"> + <repository name="package_picard_1_56_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="99a28567c3a3"/> </package> <package name="samtools" version="0.1.18"> - <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="171cd8bc208d"/> </package> -</tool_dependency> +</tool_dependency> \ No newline at end of file