Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
changeset 0:c669787306ae draft
Uploaded
| author | devteam |
|---|---|
| date | Tue, 03 Feb 2015 10:08:46 -0500 |
| parents | |
| children | bca4c608408c |
| files | README data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml data_manager_conf.xml test-data/phiX174.data_manager_json test-data/phiX174.fasta tool-data/all_fasta.loc.sample tool-data/dbkeys.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 9 files changed, 679 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Feb 03 10:08:46 2015 -0500 @@ -0,0 +1,1 @@ +Creates a New dbkey entry with .len files in __dbkeys__ and populates all_fasta tool datatables. \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py Tue Feb 03 10:08:46 2015 -0500 @@ -0,0 +1,415 @@ +#!/usr/bin/env python +#Dan Blankenberg + +import sys +import os +import tempfile +import shutil +import optparse +import urllib2 +#import uuid +from ftplib import FTP +import tarfile +import zipfile +import gzip +import bz2 + +from json import loads, dumps + + +CHUNK_SIZE = 2**20 #1mb + +def cleanup_before_exit( tmp_dir ): + if tmp_dir and os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit(1) + +def get_dbkey_dbname_id_name( params, dbkey_description=None ): + dbkey = params['param_dict']['dbkey_source']['dbkey'] + #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: + sequence_id = dbkey #uuid.uuid4() generate and use an uuid instead? + + if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new': + dbkey_name = params['param_dict']['dbkey_source']['dbkey_name'] + if not dbkey_name: + dbkey_name = dbkey + else: + dbkey_name = None + + sequence_name = params['param_dict']['sequence_name'] + if not sequence_name: + sequence_name = dbkey_description + if not sequence_name: + sequence_name = dbkey + return dbkey, dbkey_name, sequence_id, sequence_name + +def _get_files_in_ftp_path( ftp, path ): + path_contents = [] + ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append ) + return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ] + +def _get_stream_readers_for_tar( file_obj, tmp_dir ): + fasta_tar = tarfile.open( fileobj=file_obj, mode='r:*' ) + return filter( lambda x: x is not None, [ fasta_tar.extractfile( member ) for member in fasta_tar.getmembers() ] ) + +def _get_stream_readers_for_zip( file_obj, tmp_dir ): + fasta_zip = zipfile.ZipFile( file_obj, 'r' ) + rval = [] + for member in fasta_zip.namelist(): + fasta_zip.extract( member, tmp_dir ) + rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) ) + return rval + +def _get_stream_readers_for_gzip( file_obj, tmp_dir ): + return [ gzip.GzipFile( fileobj=file_obj, mode='rb' ) ] + +def _get_stream_readers_for_bz2( file_obj, tmp_dir ): + return [ bz2.BZ2File( file_obj.name, 'rb' ) ] + +def sort_fasta( fasta_filename, sort_method, params ): + if sort_method is None: + return + assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method ) + return SORTING_METHODS[ sort_method ]( fasta_filename, params ) + +def _move_and_index_fasta_for_sorting( fasta_filename ): + unsorted_filename = tempfile.NamedTemporaryFile().name + 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 = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), 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 _sort_fasta_as_is( fasta_filename, params ): + return + +def _sort_fasta_lexicographical( fasta_filename, params ): + ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename ) + sorted_names = sorted( fasta_offsets.keys() ) + if sorted_names == current_order: + shutil.move( unsorted_filename, fasta_filename ) + else: + _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename ) + +def _sort_fasta_gatk( fasta_filename, params ): + #This method was added by reviewer request. + ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename ) + sorted_names = map( str, range( 1, 23 ) ) + [ 'X', 'Y' ] + #detect if we have chrN, or just N + has_chr = False + for chrom in sorted_names: + if "chr%s" % chrom in current_order: + has_chr = True + break + + if has_chr: + sorted_names = map( lambda x: "chr%s" % x, sorted_names) + sorted_names.insert( 0, "chrM" ) + else: + sorted_names.insert( 0, "MT" ) + sorted_names.extend( map( lambda x: "%s_random" % x, sorted_names ) ) + + existing_sorted_names = [] + for name in sorted_names: + if name in current_order: + 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 ) + + if existing_sorted_names == current_order: + shutil.move( unsorted_filename, fasta_filename ) + else: + _write_sorted_fasta( existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename ) + +def _sort_fasta_custom( fasta_filename, params ): + ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename ) + sorted_names = [] + for id_repeat in params['param_dict']['sorting']['sequence_identifiers']: + sorted_names.append( id_repeat[ 'identifier' ] ) + handle_not_listed = params['param_dict']['sorting']['handle_not_listed']['handle_not_listed_selector'] + if handle_not_listed.startswith( 'keep' ): + add_list = [] + for name in current_order: + if name not in sorted_names: + add_list.append( name ) + if add_list: + if handle_not_listed == 'keep_append': + sorted_names.extend( add_list ) + else: + add_list.extend( sorted_names ) + sorted_names = add_list + if sorted_names == current_order: + shutil.move( unsorted_filename, fasta_filename ) + else: + _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename ) + +def download_from_ucsc( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): + UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu' + UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/' + COMPRESSED_EXTENSIONS = [ ( '.tar.gz', _get_stream_readers_for_tar ), ( '.tar.bz2', _get_stream_readers_for_tar ), ( '.zip', _get_stream_readers_for_zip ), ( '.fa.gz', _get_stream_readers_for_gzip ), ( '.fa.bz2', _get_stream_readers_for_bz2 ) ] + + email = params['param_dict']['__user_email__'] + if not email: + email = 'anonymous@example.com' + + ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey + UCSC_CHROM_FA_FILENAMES = [ '%s.chromFa' % ucsc_dbkey, 'chromFa' ] + + ftp = FTP( UCSC_FTP_SERVER ) + ftp.login( 'anonymous', email ) + + ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey + path_contents = _get_files_in_ftp_path( ftp, ucsc_path ) + + ucsc_file_name = None + get_stream_reader = None + ext = None + ucsc_chrom_fa_filename = None + for ucsc_chrom_fa_filename in UCSC_CHROM_FA_FILENAMES: + for ext, get_stream_reader in COMPRESSED_EXTENSIONS: + if "%s%s" % ( ucsc_chrom_fa_filename, ext ) in path_contents: + ucsc_file_name = "%s%s%s" % ( ucsc_path, ucsc_chrom_fa_filename, ext ) + break + if ucsc_file_name: + break + + if not ucsc_file_name: + raise Exception( 'Unable to determine filename for UCSC Genome for %s: %s' % ( ucsc_dbkey, path_contents ) ) + + + tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ucsc-' ) + ucsc_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( ucsc_chrom_fa_filename, ext ) ) + + fasta_base_filename = "%s.fa" % sequence_id + fasta_filename = os.path.join( target_directory, fasta_base_filename ) + fasta_writer = open( fasta_filename, 'wb+' ) + + tmp_extract_dir = os.path.join ( tmp_dir, 'extracted_fasta' ) + os.mkdir( tmp_extract_dir ) + + tmp_fasta = open( ucsc_fasta_filename, 'wb+' ) + + ftp.retrbinary( 'RETR %s' % ucsc_file_name, tmp_fasta.write ) + + tmp_fasta.flush() + tmp_fasta.seek( 0 ) + + fasta_readers = get_stream_reader( tmp_fasta, tmp_extract_dir ) + + for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ): + if data_table_entry: + _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) + + for fasta_reader in fasta_readers: + fasta_reader.close() + tmp_fasta.close() + cleanup_before_exit( tmp_dir ) + +def download_from_ncbi( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): + NCBI_DOWNLOAD_URL = 'http://togows.dbcls.jp/entry/ncbi-nucleotide/%s.fasta' #FIXME: taken from dave's genome manager...why some japan site? + + requested_identifier = params['param_dict']['reference_source']['requested_identifier'] + url = NCBI_DOWNLOAD_URL % requested_identifier + fasta_readers = urllib2.urlopen( url ) + + for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ): + if data_table_entry: + _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) + +def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): + #TODO: we should automatically do decompression here + urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) ) + fasta_readers = [ urllib2.urlopen( url ) for url in urls ] + + for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ): + if data_table_entry: + _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) + +def download_from_history( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): + #TODO: allow multiple FASTA input files + input_filename = params['param_dict']['reference_source']['input_fasta'] + if isinstance( input_filename, list ): + fasta_readers = [ open( filename, 'rb' ) for filename in input_filename ] + else: + fasta_readers = open( input_filename ) + + for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ): + if data_table_entry: + _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) + +def copy_from_directory( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): + input_filename = params['param_dict']['reference_source']['fasta_filename'] + create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink' + if create_symlink: + data_table_entries = _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ) + else: + if isinstance( input_filename, list ): + fasta_readers = [ open( filename, 'rb' ) for filename in input_filename ] + else: + fasta_readers = open( input_filename ) + data_table_entries = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ) + for data_table_name, data_table_entry in data_table_entries: + if data_table_entry: + _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) + +def _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ): + 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( 'all_fasta', [] ) + data_manager_dict['data_tables'][data_table_name].append( data_table_entry ) + return data_manager_dict + +def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, close_stream=True ): + fasta_base_filename = "%s.fa" % sequence_id + fasta_filename = os.path.join( target_directory, fasta_base_filename ) + fasta_writer = open( fasta_filename, 'wb+' ) + + if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1: + fasta_stream = fasta_stream[0] + + if isinstance( fasta_stream, list ): + last_char = None + for fh in fasta_stream: + if last_char not in [ None, '\n', '\r' ]: + fasta_writer.write( '\n' ) + while True: + data = fh.read( CHUNK_SIZE ) + if data: + fasta_writer.write( data ) + last_char = data[-1] + else: + break + if close_stream: + fh.close() + else: + while True: + data = fasta_stream.read( CHUNK_SIZE ) + if data: + fasta_writer.write( data ) + else: + break + if close_stream: + fasta_stream.close() + + fasta_writer.close() + + sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params ) + + dbkey_dict = None + if dbkey_name: + #do len calc here + len_base_name = "%s.len" % ( dbkey ) + compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True ) + dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path=len_base_name ) + + return [ ( '__dbkeys__', dbkey_dict ), ( 'all_fasta', dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ] + +def compute_fasta_length( fasta_file, out_file, keep_first_word=False ): + + infile = fasta_file + out = open( out_file, 'w') + + fasta_title = '' + seq_len = 0 + + first_entry = True + + for line in open( infile ): + line = line.strip() + if not line or line.startswith( '#' ): + continue + if line[0] == '>': + if first_entry == False: + if keep_first_word: + fasta_title = fasta_title.split()[0] + out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) ) + else: + first_entry = False + fasta_title = line + seq_len = 0 + else: + seq_len += len(line) + + # last fasta-entry + if keep_first_word: + fasta_title = fasta_title.split()[0] + out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) ) + out.close() + +def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): + fasta_base_filename = "%s.fa" % sequence_id + fasta_filename = os.path.join( target_directory, fasta_base_filename ) + os.symlink( input_filename, fasta_filename ) + + dbkey_dict = None + if dbkey_name: + #do len calc here + len_base_name = "%s.len" % ( dbkey ) + compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True ) + dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path=len_base_name ) + + return [ ( '__dbkeys__', dbkey_dict ), ( 'all_fasta', dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ] + + + + +REFERENCE_SOURCE_TO_DOWNLOAD = dict( ucsc=download_from_ucsc, ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory ) + +SORTING_METHODS = dict( as_is=_sort_fasta_as_is, lexicographical=_sort_fasta_lexicographical, gatk=_sort_fasta_gatk, custom=_sort_fasta_custom ) + +def main(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' ) + (options, args) = parser.parse_args() + + filename = args[0] + + params = loads( open( filename ).read() ) + target_directory = params[ 'output_data' ][0]['extra_files_path'] + os.mkdir( target_directory ) + data_manager_dict = {} + + dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name( params, dbkey_description=options.dbkey_description ) + + if dbkey in [ None, '', '?' ]: + raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) + + #Fetch the FASTA + REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ) + + #save info to json file + open( filename, 'wb' ).write( dumps( data_manager_dict ) ) + +if __name__ == "__main__": main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Tue Feb 03 10:08:46 2015 -0500 @@ -0,0 +1,116 @@ +<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.1" tool_type="manage_data"> + <description>fetching</description> + <command interpreter="python">data_manager_fetch_genome_all_fasta_dbkeys.py "${out_file}" + #if str( $dbkey_source.dbkey_source_selector ) == 'existing': + --dbkey_description ${ dbkey_source.dbkey.get_display_text() } + #else + --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" + #end if + + </command> + <inputs> + <conditional name="dbkey_source"> + <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one."> + <option value="existing" selected="True">Existing</option> + <option value="new">New</option> + </param> + <when value="existing"> + <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> + </when> + <when value="new"> + <param type="text" name="dbkey" value="" label="dbkey" optional="False" /> + <param type="text" name="dbkey_name" value="" label="Display name for dbkey" /> + </when> + </conditional> + + <param type="text" name="sequence_name" value="" label="Name of sequence" /> + <param type="text" name="sequence_id" value="" label="ID for sequence" /> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="ucsc" selected="True">UCSC</option> + <option value="ncbi">NCBI</option> + <option value="url">URL</option> + <option value="history">History</option> + <option value="directory">Directory on Server</option> + </param> + <when value="ucsc"> + <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" /> + </when> + <when value="ncbi"> + <param type="text" name="requested_identifier" value="" label="NCBI identifier" optional="False" /> + </when> + <when value="url"> + <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> + </when> + <when value="history"> + <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> + </when> + <when value="directory"> + <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" /> + <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" /> + </when> + </conditional> + <conditional name="sorting"> + <param name="sort_selector" type="select" label="Choose the source for the reference genome"> + <option value="as_is" selected="True">As is</option> + <option value="lexicographical">Lexicographical</option> + <option value="gatk">GATK</option> + <option value="custom">Custom</option> + </param> + <when value="as_is"> + </when> + <when value="lexicographical"> + </when> + <when value="gatk"> + </when> + <when value="custom"> + <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1"> + <param type="text" name="identifier" value="" label="Sequence Identifier" optional="False" /> + </repeat> + <conditional name="handle_not_listed"> + <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers"> + <option value="discard" selected="True">Discard</option> + <option value="keep_append">Keep and Append</option> + <option value="keep_prepend">Keep and Prepend</option> + </param> + <when value="discard"> + </when> + <when value="keep_append"> + </when> + <when value="keep_prepend"> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <tests> + <!-- TODO: need some way to test that new entry was added to data table --> + <test> + <param name="dbkey" value="anoGam1"/> + <param name="sequence_name" value=""/> + <param name="sequence_desc" value=""/> + <param name="sequence_id" value=""/> + <param name="reference_source_selector" value="history"/> + <param name="input_fasta" value="phiX174.fasta"/> + <param name="sort_selector" value="as_is"/> + <output name="out_file" file="phiX174.data_manager_json"/> + </test> + </tests> + <help> +**What it does** + +Fetches a reference genome from various sources (UCSC, NCBI, URL, Galaxy History, or a server directory) and populates the "all_fasta" data table. + +------ + + + +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Feb 03 10:08:46 2015 -0500 @@ -0,0 +1,36 @@ +<?xml version="1.0"?> +<data_managers> + + <data_manager tool_file="data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml" id="fetch_genome_all_fasta_dbkeys"> + <data_table name="all_fasta"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" output_ref="out_file" > + <move type="file"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/seq/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/seq/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="__dbkeys__"> + <output> + <column name="value" /> + <column name="name" /> + <column name="len_path" output_ref="out_file" > + <move type="file"> + <source>${len_path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/len/${len_path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/len/${len_path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> + +</data_managers>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.data_manager_json Tue Feb 03 10:08:46 2015 -0500 @@ -0,0 +1,1 @@ +{"data_tables": {"all_fasta": [{"path": "anoGam1.fa", "dbkey": "anoGam1", "name": "A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1)", "value": "anoGam1"}]}} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.fasta Tue Feb 03 10:08:46 2015 -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/tool-data/all_fasta.loc.sample Tue Feb 03 10:08:46 2015 -0500 @@ -0,0 +1,18 @@ +#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. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/dbkeys.loc.sample Tue Feb 03 10:08:46 2015 -0500 @@ -0,0 +1,1 @@ +#<dbkey> <display_name> <len_file_path> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Feb 03 10:08:46 2015 -0500 @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> + <!-- Locations of dbkeys and len files under genome directory --> + <table name="__dbkeys__" comment_char="#"> + <columns>value, name, len_path</columns> + <file path="tool-data/dbkeys.loc" /> + </table> +</tables>