| Next changeset 1:bca4c608408c (2015-02-03) |
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Commit message:
Uploaded |
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added:
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 |
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| diff -r 000000000000 -r c669787306ae README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Feb 03 10:08:46 2015 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r c669787306ae data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py --- /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 |
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| b'@@ -0,0 +1,415 @@\n+#!/usr/bin/env python\n+#Dan Blankenberg\n+\n+import sys\n+import os\n+import tempfile\n+import shutil\n+import optparse\n+import urllib2\n+#import uuid\n+from ftplib import FTP\n+import tarfile\n+import zipfile\n+import gzip\n+import bz2\n+\n+from json import loads, dumps\n+\n+\n+CHUNK_SIZE = 2**20 #1mb\n+\n+def cleanup_before_exit( tmp_dir ):\n+ if tmp_dir and os.path.exists( tmp_dir ):\n+ shutil.rmtree( tmp_dir )\n+\n+def stop_err(msg):\n+ sys.stderr.write(msg)\n+ sys.exit(1)\n+ \n+def get_dbkey_dbname_id_name( params, dbkey_description=None ):\n+ dbkey = params[\'param_dict\'][\'dbkey_source\'][\'dbkey\']\n+ #TODO: ensure sequence_id is unique and does not already appear in location file\n+ sequence_id = params[\'param_dict\'][\'sequence_id\']\n+ if not sequence_id:\n+ sequence_id = dbkey #uuid.uuid4() generate and use an uuid instead?\n+ \n+ if params[\'param_dict\'][\'dbkey_source\'][\'dbkey_source_selector\'] == \'new\':\n+ dbkey_name = params[\'param_dict\'][\'dbkey_source\'][\'dbkey_name\']\n+ if not dbkey_name:\n+ dbkey_name = dbkey\n+ else:\n+ dbkey_name = None\n+ \n+ sequence_name = params[\'param_dict\'][\'sequence_name\']\n+ if not sequence_name:\n+ sequence_name = dbkey_description\n+ if not sequence_name:\n+ sequence_name = dbkey\n+ return dbkey, dbkey_name, sequence_id, sequence_name\n+\n+def _get_files_in_ftp_path( ftp, path ):\n+ path_contents = []\n+ ftp.retrlines( \'MLSD %s\' % ( path ), path_contents.append )\n+ return [ line.split( \';\' )[ -1 ].lstrip() for line in path_contents ]\n+\n+def _get_stream_readers_for_tar( file_obj, tmp_dir ):\n+ fasta_tar = tarfile.open( fileobj=file_obj, mode=\'r:*\' )\n+ return filter( lambda x: x is not None, [ fasta_tar.extractfile( member ) for member in fasta_tar.getmembers() ] )\n+\n+def _get_stream_readers_for_zip( file_obj, tmp_dir ):\n+ fasta_zip = zipfile.ZipFile( file_obj, \'r\' )\n+ rval = []\n+ for member in fasta_zip.namelist():\n+ fasta_zip.extract( member, tmp_dir )\n+ rval.append( open( os.path.join( tmp_dir, member ), \'rb\' ) )\n+ return rval\n+\n+def _get_stream_readers_for_gzip( file_obj, tmp_dir ):\n+ return [ gzip.GzipFile( fileobj=file_obj, mode=\'rb\' ) ]\n+\n+def _get_stream_readers_for_bz2( file_obj, tmp_dir ):\n+ return [ bz2.BZ2File( file_obj.name, \'rb\' ) ]\n+\n+def sort_fasta( fasta_filename, sort_method, params ):\n+ if sort_method is None:\n+ return\n+ assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method )\n+ return SORTING_METHODS[ sort_method ]( fasta_filename, params )\n+\n+def _move_and_index_fasta_for_sorting( fasta_filename ):\n+ unsorted_filename = tempfile.NamedTemporaryFile().name\n+ shutil.move( fasta_filename, unsorted_filename )\n+ fasta_offsets = {}\n+ unsorted_fh = open( unsorted_filename )\n+ while True:\n+ offset = unsorted_fh.tell()\n+ line = unsorted_fh.readline()\n+ if not line:\n+ break\n+ if line.startswith( ">" ):\n+ line = line.split( None, 1 )[0][1:]\n+ fasta_offsets[ line ] = offset\n+ unsorted_fh.close()\n+ current_order = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), fasta_offsets.items() ) ) )\n+ return ( unsorted_filename, fasta_offsets, current_order )\n+\n+def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ):\n+ unsorted_fh = open( unsorted_fasta_filename )\n+ sorted_fh = open( sorted_fasta_filename, \'wb+\' )\n+ \n+ for name in sorted_names:\n+ offset = fasta_offsets[ name ]\n+ unsorted_fh.seek( offset )\n+ sorted_fh.write( unsorted_fh.readline() )\n+ while True:\n+ line = unsorted_fh.readline()\n+ if not line or line.startswith( ">" ):\n+ break\n+ sorted_fh.write( line )\n+ unsorted_fh.close()\n+ sorted_fh.close()\n+\n+def _sort_fasta_as_is( fasta_filename, params ):\n+ return\n'..b' else:\n+ while True:\n+ data = fasta_stream.read( CHUNK_SIZE )\n+ if data:\n+ fasta_writer.write( data )\n+ else:\n+ break\n+ if close_stream:\n+ fasta_stream.close()\n+ \n+ fasta_writer.close()\n+ \n+ sort_fasta( fasta_filename, params[\'param_dict\'][\'sorting\'][\'sort_selector\'], params )\n+ \n+ dbkey_dict = None\n+ if dbkey_name:\n+ #do len calc here\n+ len_base_name = "%s.len" % ( dbkey )\n+ compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True )\n+ dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path=len_base_name )\n+ \n+ return [ ( \'__dbkeys__\', dbkey_dict ), ( \'all_fasta\', dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]\n+\n+def compute_fasta_length( fasta_file, out_file, keep_first_word=False ):\n+\n+ infile = fasta_file\n+ out = open( out_file, \'w\')\n+\n+ fasta_title = \'\'\n+ seq_len = 0\n+\n+ first_entry = True\n+\n+ for line in open( infile ):\n+ line = line.strip()\n+ if not line or line.startswith( \'#\' ):\n+ continue\n+ if line[0] == \'>\':\n+ if first_entry == False:\n+ if keep_first_word:\n+ fasta_title = fasta_title.split()[0]\n+ out.write( "%s\\t%d\\n" % ( fasta_title[ 1: ], seq_len ) )\n+ else:\n+ first_entry = False\n+ fasta_title = line\n+ seq_len = 0\n+ else:\n+ seq_len += len(line)\n+\n+ # last fasta-entry\n+ if keep_first_word:\n+ fasta_title = fasta_title.split()[0]\n+ out.write( "%s\\t%d\\n" % ( fasta_title[ 1: ], seq_len ) )\n+ out.close()\n+\n+def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):\n+ fasta_base_filename = "%s.fa" % sequence_id\n+ fasta_filename = os.path.join( target_directory, fasta_base_filename )\n+ os.symlink( input_filename, fasta_filename )\n+ \n+ dbkey_dict = None\n+ if dbkey_name:\n+ #do len calc here\n+ len_base_name = "%s.len" % ( dbkey )\n+ compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True )\n+ dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path=len_base_name )\n+ \n+ return [ ( \'__dbkeys__\', dbkey_dict ), ( \'all_fasta\', dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]\n+\n+\n+\n+\n+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 )\n+\n+SORTING_METHODS = dict( as_is=_sort_fasta_as_is, lexicographical=_sort_fasta_lexicographical, gatk=_sort_fasta_gatk, custom=_sort_fasta_custom )\n+\n+def main():\n+ #Parse Command Line\n+ parser = optparse.OptionParser()\n+ parser.add_option( \'-d\', \'--dbkey_description\', dest=\'dbkey_description\', action=\'store\', type="string", default=None, help=\'dbkey_description\' )\n+ (options, args) = parser.parse_args()\n+ \n+ filename = args[0]\n+ \n+ params = loads( open( filename ).read() )\n+ target_directory = params[ \'output_data\' ][0][\'extra_files_path\']\n+ os.mkdir( target_directory )\n+ data_manager_dict = {}\n+ \n+ dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name( params, dbkey_description=options.dbkey_description ) \n+ \n+ if dbkey in [ None, \'\', \'?\' ]:\n+ raise Exception( \'"%s" is not a valid dbkey. You must specify a valid dbkey.\' % ( dbkey ) )\n+ \n+ #Fetch the FASTA\n+ 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 )\n+ \n+ #save info to json file\n+ open( filename, \'wb\' ).write( dumps( data_manager_dict ) )\n+ \n+if __name__ == "__main__": main()\n' |
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| diff -r 000000000000 -r c669787306ae data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml --- /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 |
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| @@ -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> |
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| diff -r 000000000000 -r c669787306ae data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Feb 03 10:08:46 2015 -0500 |
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| @@ -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> |
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| diff -r 000000000000 -r c669787306ae test-data/phiX174.data_manager_json --- /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 |
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| @@ -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 |
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| diff -r 000000000000 -r c669787306ae test-data/phiX174.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.fasta Tue Feb 03 10:08:46 2015 -0500 |
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| @@ -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 + |
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| diff -r 000000000000 -r c669787306ae tool-data/all_fasta.loc.sample --- /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 |
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| @@ -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. +# |
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| diff -r 000000000000 -r c669787306ae tool-data/dbkeys.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/dbkeys.loc.sample Tue Feb 03 10:08:46 2015 -0500 |
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| @@ -0,0 +1,1 @@ +#<dbkey> <display_name> <len_file_path> \ No newline at end of file |
| b |
| diff -r 000000000000 -r c669787306ae tool_data_table_conf.xml.sample --- /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 |
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| @@ -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> |