# HG changeset patch
# User devteam
# Date 1422975411 18000
# Node ID 00c5a5563f2922a35292669255cf588f20ae9dc4
Uploaded
diff -r 000000000000 -r 00c5a5563f29 .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Tue Feb 03 09:56:51 2015 -0500
@@ -0,0 +1,4 @@
+# repository published to https://toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta
+owner: devteam
+name: data_manager_fetch_genome_all_fasta
+
\ No newline at end of file
diff -r 000000000000 -r 00c5a5563f29 data_manager/data_manager_fetch_genome_all_fasta.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_genome_all_fasta.py Tue Feb 03 09:56:51 2015 -0500
@@ -0,0 +1,355 @@
+#!/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_id_name( params, dbkey_description=None ):
+ dbkey = params['param_dict']['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?
+
+ sequence_name = params['param_dict']['sequence_name']
+ if not sequence_name:
+ sequence_name = dbkey_description
+ if not sequence_name:
+ sequence_name = dbkey
+ return dbkey, 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, 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 )
+
+ data_table_entry = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, sequence_id, sequence_name, params )
+ _add_data_table_entry( data_manager_dict, data_table_entry )
+
+ 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, 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_reader = urllib2.urlopen( url )
+
+ data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, dbkey, sequence_id, sequence_name, params )
+ _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def download_from_url( data_manager_dict, params, target_directory, dbkey, 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_reader = [ urllib2.urlopen( url ) for url in urls ]
+
+ data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, dbkey, sequence_id, sequence_name, params )
+ _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def download_from_history( data_manager_dict, params, target_directory, dbkey, 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_reader = [ open( filename, 'rb' ) for filename in input_filename ]
+ else:
+ fasta_reader = open( input_filename )
+
+ data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, dbkey, sequence_id, sequence_name, params )
+ _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def copy_from_directory( data_manager_dict, params, target_directory, dbkey, 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_entry = _create_symlink( input_filename, target_directory, dbkey, sequence_id, sequence_name )
+ else:
+ if isinstance( input_filename, list ):
+ fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
+ else:
+ fasta_reader = open( input_filename )
+ data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, dbkey, sequence_id, sequence_name, params )
+ _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def _add_data_table_entry( data_manager_dict, data_table_entry ):
+ data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+ data_manager_dict['data_tables']['all_fasta'] = data_manager_dict['data_tables'].get( 'all_fasta', [] )
+ data_manager_dict['data_tables']['all_fasta'].append( data_table_entry )
+ return data_manager_dict
+
+def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, 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 )
+
+ return dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename )
+
+def _create_symlink( input_filename, target_directory, dbkey, 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 )
+ return 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, sequence_id, sequence_name = get_dbkey_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, sequence_id, sequence_name )
+
+ #save info to json file
+ open( filename, 'wb' ).write( dumps( data_manager_dict ) )
+
+if __name__ == "__main__": main()
diff -r 000000000000 -r 00c5a5563f29 data_manager/data_manager_fetch_genome_all_fasta.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_genome_all_fasta.xml Tue Feb 03 09:56:51 2015 -0500
@@ -0,0 +1,97 @@
+
+ fetching
+ data_manager_fetch_genome_all_fasta.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() }
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+**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.
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diff -r 000000000000 -r 00c5a5563f29 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Tue Feb 03 09:56:51 2015 -0500
@@ -0,0 +1,22 @@
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diff -r 000000000000 -r 00c5a5563f29 test-data/phiX174.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174.fasta Tue Feb 03 09:56:51 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
+
diff -r 000000000000 -r 00c5a5563f29 test-data/phiX174_as_anoGam1.data_manager_json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174_as_anoGam1.data_manager_json Tue Feb 03 09:56:51 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
diff -r 000000000000 -r 00c5a5563f29 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 09:56:51 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):
+#
+#
+#
+#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.
+#
diff -r 000000000000 -r 00c5a5563f29 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 09:56:51 2015 -0500
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, name, path
+
+
+