# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent kpvincent@bx.psu.edu # Date 1289194982 18000 # Node ID 7ca26b1cc9b6fd67364a6c6af6005ceecaa3f45b # Parent 535d276c92bcc35e563c4ce5a2351f562f451132 Added a sample loc file listing all fasta files and a script to generate the file given a base genome directory.

--- /dev/null +++ b/tool-data/all_fasta.loc.sample @@ -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 +++ b/scripts/loc_files/create_all_fasta_loc.py @@ -0,0 +1,300 @@ +import optparse, os, sys +import elementtree.ElementTree as etree + +""" +Generates a loc file containing names of all the fasta files that match the +name of the genome subdirectory they're in. +Assumptions: + - fasta files should be named the same as the genome subdirectory they're + in, with the possible addition of a recognized variant (canon, full, etc.) + - for "variants" (like full, canon[ical], chrM, etc.) the naming needs to be + consistent and specific: + - <genome_name><variant>, like hg19canon, hg19full, or hg19chrM +Normal usage: +create_all_fasta_loc.py -f unmatching_fasta.txt -i seq + +usage: %prog [options] + -d, --data-table-xml=d: The name of the data table configuration file to get format of loc file + -t, --data-table=t: The name of the data table listed in the data table XML file + -g, --genome-dir=g: Genome directory to look in + -e, --exemptions=e: Comma-separated list of genome dir subdirectories to not look in + -i, --inspect-dirs=i: Comma-separated list of subdirectories inside genome dirs to look in (default is all) + -x, --fasta-exts=x: Comma-separated list of all fasta extensions to list + -s, --loc-sample=s: The name of the sample loc file (to copy text into top of output loc file) + -f, --unmatching-fasta=f: Name of file to output non-matching fasta files to, if included + -v, --variants=v: Comma-separated list of recognized variants of fasta file names + -a, --append=a: Append to existing all_fasta.loc file rather than create new + -p, --sample-text=p: Copy over text from all_fasta.loc.sample file (false if set to append) +""" + +DEFAULT_TOOL_DATA_TABLE_CONF = 'tool_data_table_conf.xml' +DEFAULT_ALL_FASTA_LOC_BASE = 'all_fasta' +DEFAULT_BASE_GENOME_DIR = '/afs/bx.psu.edu/depot/data/genome' +EXEMPTIONS = 'bin,tmp,lengths,equCab2_chrM,microbes' +INSPECT_DIR = None +FASTA_EXTS = '.fa,.fasta,.fna' +VARIANTS = 'chrM,chr21,full,canon,female,male,haps,nohaps' + +VARIANT_EXCLUSIONS = ':full' + +DBKEY_DESCRIPTION_MAP = { 'AaegL1': 'Mosquito (Aedes aegypti): AaegL1', + 'AgamP3': 'Mosquito (Anopheles gambiae): AgamP3', + 'anoCar1': 'Lizard (Anolis carolinensis): anoCar1', + 'anoGam1': 'Mosquito (Anopheles gambiae): anoGam1', + 'apiMel1': 'Honeybee (Apis mellifera): apiMel1', + 'apiMel2': 'Honeybee (Apis mellifera): apiMel2', + 'apiMel3': 'Honeybee (Apis mellifera): apiMel3', + 'Arabidopsis_thaliana_TAIR9': '', + 'borEut13': 'Boreoeutherian: borEut13', + 'bosTau2': 'Cow (Bos taurus): bosTau2', + 'bosTau3': 'Cow (Bos taurus): bosTau3', + 'bosTau4': 'Cow (Bos taurus): bosTau4', + 'bosTauMd3': 'Cow (Bos taurus): bosTauMd3', + 'calJac1': 'Marmoset (Callithrix jacchus): calJac1', + 'canFam1': 'Dog (Canis lupus familiaris): canFam1', + 'canFam2': 'Dog (Canis lupus familiaris): canFam2', + 'cavPor3': 'Guinea Pig (Cavia porcellus): cavPor3', + 'ce2': 'Caenorhabditis elegans: ce2', + 'ce4': 'Caenorhabditis elegans: ce4', + 'ce5': 'Caenorhabditis elegans: ce5', + 'ce6': 'Caenorhabditis elegans: ce6', + 'CpipJ1': 'Mosquito (Culex quinquefasciatus): CpipJ1', + 'danRer2': 'Zebrafish (Danio rerio): danRer2', + 'danRer3': 'Zebrafish (Danio rerio): danRer3', + 'danRer4': 'Zebrafish (Danio rerio): danRer4', + 'danRer5': 'Zebrafish (Danio rerio): danRer5', + 'danRer6': 'Zebrafish (Danio rerio): danRer6', + 'dm1': 'Fruit Fly (Drosophila melanogaster): dm1', + 'dm2': 'Fruit Fly (Drosophila melanogaster): dm2', + 'dm3': 'Fruit Fly (Drosophila melanogaster): dm3', + 'dm4': 'Fruit Fly (Drosophila melanogaster): dm', + 'dp3': 'Fruit Fly (Drosophila pseudoobscura): dp3', + 'dp4': 'Fruit Fly (Drosophila pseudoobscura): dp4', + 'droAna1': 'Fruit Fly (Drosophila ananassae): droAna1', + 'droAna2': 'Fruit Fly (Drosophila ananassae): droAna2', + 'droAna3': 'Fruit Fly (Drosophila ananassae): droAna3', + 'droEre1': 'Fruit Fly (Drosophila erecta): droEre1', + 'droEre2': 'Fruit Fly (Drosophila erecta): droEre2', + 'droGri1': 'Fruit Fly (Drosophila grimshawi): droGri1', + 'droGri2': 'Fruit Fly (Drosophila grimshawi): droGri2', + 'droMoj1': 'Fruit Fly (Drosophila mojavensis): droMoj1', + 'droMoj2': 'Fruit Fly (Drosophila mojavensis): droMoj2', + 'droMoj3': 'Fruit Fly (Drosophila mojavensis): droMoj3', + 'droPer1': 'Fruit Fly (Drosophila persimilis): droPer1', + 'droSec1': 'Fruit Fly (Drosophila sechellia): droSec1', + 'droSim1': 'Fruit Fly (Drosophila simulans): droSim1', + 'droVir1': 'Fruit Fly (Drosophila virilis): droVir1', + 'droVir2': 'Fruit Fly (Drosophila virilis): droVir2', + 'droVir3': 'Fruit Fly (Drosophila virilis): droVir3', + 'droYak1': 'Fruit Fly (Drosophila yakuba): droYak1', + 'droYak2': 'Fruit Fly (Drosophila yakuba): droYak2', + 'echTel1': 'Tenrec (Echinops telfairi): echTel1', + 'equCab1': 'Horse (Equus caballus): equCab1', + 'equCab2': 'Horse (Equus caballus): equCab2', + 'eriEur1': 'Hedgehog (Erinaceus europaeus): eriEur1', + 'felCat3': 'Cat (Felis catus): felCat3', + 'fr1': 'Fugu (Takifugu rubripes): fr1', + 'fr2': 'Fugu (Takifugu rubripes): fr2', + 'galGal2': 'Chicken (Gallus gallus): galGal2', + 'galGal3': 'Chicken (Gallus gallus): galGal3', + 'gasAcu1': 'Stickleback (Gasterosteus aculeatus): gasAcu1', + 'hg16': 'Human (Homo sapiens): hg16', + 'hg17': 'Human (Homo sapiens): hg17', + 'hg18': 'Human (Homo sapiens): hg18', + 'hg19': 'Human (Homo sapiens): hg19', + 'IscaW1': 'Deer Tick (Ixodes scapularis): IscaW1', + 'lMaj5': 'Leishmania major: lMaj5', + 'mm5': 'Mouse (Mus musculus): mm5', + 'mm6': 'Mouse (Mus musculus): mm6', + 'mm7': 'Mouse (Mus musculus): mm7', + 'mm8': 'Mouse (Mus musculus): mm8', + 'mm9': 'Mouse (Mus musculus): mm9', + 'monDom4': 'Opossum (Monodelphis domestica): monDom4', + 'monDom5': 'Opossum (Monodelphis domestica): monDom5', + 'ornAna1': 'Platypus (Ornithorhynchus anatinus): ornAna1', + 'oryCun1': 'Rabbit (Oryctolagus cuniculus): oryCun1', + 'oryLat1': 'Medaka (Oryzias latipes): oryLat1', + 'oryLat2': 'Medaka (Oryzias latipes): oryLat2', + 'oryza_sativa_japonica_nipponbare_IRGSP4.0': 'Rice (Oryza sativa L. ssp. japonica var. Nipponbare): IRGSP4.0', + 'otoGar1': 'Bushbaby (Otolemur garnetti): otoGar1', + 'panTro1': 'Chimpanzee (Pan troglodytes): panTro1', + 'panTro2': 'Chimpanzee (Pan troglodytes): panTro2', + 'petMar1': 'Lamprey (Petromyzon marinus): petMar1', + 'phiX': 'phiX174 (AF176034)', + 'PhumU1': 'Head Louse (Pediculus humanus): PhumU1', + 'ponAbe2': 'Orangutan (Pongo pygmaeus abelii): ponAbe2', + 'pUC18': 'pUC18 (L09136)', + 'rheMac2': 'Rhesus Macaque (Macaca mulatta): rheMac2', + 'rn3': 'Rat (Rattus norvegicus): rn3', + 'rn4': 'Rat (Rattus norvegicus): rn4', + 'sacCer1': 'Yeast (Saccharomyces cerevisiae): sacCer1', + 'sacCer2': 'Yeast (Saccharomyces cerevisiae): sacCer2', + 'sorAra1': 'Common Shrew (Sorex araneus): sorAra1', + 'Sscrofa9.58': 'Pig (Sus scrofa): Sscrofa9.58', + 'strPur2': 'Purple Sea Urchin (Strongylocentrotus purpuratus): strPur2', + 'susScr2': 'Pig (Sus scrofa): susScr2', + 'taeGut1': 'Zebra Finch (Taeniopygia guttata): taeGut1', + 'tetNig1': 'Tetraodon (Tetraodon nigroviridis): tetNig1', + 'tetNig2': 'Tetraodon (Tetraodon nigroviridis): tetNig2', + 'tupBel1': 'Tree Shrew (Tupaia belangeri): tupBel1', + 'venter1': 'Human (J. Craig Venter): venter1', + 'xenTro2': 'Frog (Xenopus tropicalis): xenTro2' + } + +VARIANT_MAP = { 'canon': 'Canonical', + 'full': 'Full', + 'female': 'Female', + 'male': 'Male' + } + +# alphabetize ignoring case +def caseless_compare( a, b ): + au = a.upper() + bu = b.upper() + if au > bu: + return 1 + elif au == bu: + return 0 + elif au < bu: + return -1 + +def __main__(): + # command line variables + parser = optparse.OptionParser() + parser.add_option( '-d', '--data-table-xml', dest='data_table_xml', type='string', default=DEFAULT_TOOL_DATA_TABLE_CONF, help='The name of the data table configuration file to get format of loc file' ) + parser.add_option( '-t', '--data-table', dest='data_table_name', type='string', default=DEFAULT_ALL_FASTA_LOC_BASE, help='The name of the data table listed in the data table XML file' ) + parser.add_option( '-g', '--genome_dir', dest='genome_dir', type='string', default=DEFAULT_BASE_GENOME_DIR, help='Genome directory to look in' ) + parser.add_option( '-e', '--exemptions', dest='exemptions', type='string', default=EXEMPTIONS, help='Comma-separated list of subdirectories in genome dir to not look in' ) + parser.add_option( '-i', '--inspect-dir', dest='inspect_dir', type='string', default=INSPECT_DIR, help='Comma-separated list of subdirectories inside genome dirs to look in (default is all)' ) + parser.add_option( '-x', '--fasta_exts', dest='fasta_exts', type='string', default=FASTA_EXTS, help='Comma-separated list of all fasta extensions to list' ) + parser.add_option( '-s', '--loc-sample', dest='loc_sample_name', type='string', help='The name of the sample loc file (to copy text into top of output loc file)' ) + parser.add_option( '-f', '--unmatching-fasta', dest='unmatching_fasta', type='string', default=None, help='Name of file to output non-matching fasta files to' ) + parser.add_option( '-v', '--variants', dest='variants', type='string', default=VARIANTS, help='Comma-separated list of recognized variants of fasta file names' ) + parser.add_option( '-n', '--variant-exclusions', dest='variant_exclusions', type='string', default=VARIANT_EXCLUSIONS, help="List of files to exclude because they're duplicated by a variants; of the format: '<variant_to_keep_1>:<variant_to_remove_1>[,<variant_to_remove_2>[,...]][;<variant_to_keep_2>:<variant_to_remove_1>[,<variant_to_remove_2>[,...]]]'; default ':(full)' (if non-variant version present (like 'hg19'), full version (like 'hg19full') will be thrown out)" ) + parser.add_option( '-a', '--append', dest='append', action='store_true', default=False, help='Append to existing all_fasta.loc file rather than create new' ) + parser.add_option( '-p', '--sample-text', dest='sample_text', action='store_true', default='True', help='Copy over text from all_fasta.loc.sample file (false if set to append)' ) + (options, args) = parser.parse_args() + + exemptions = [ e.strip() for e in options.exemptions.split( ',' ) ] + fasta_exts = [ x.strip() for x in options.fasta_exts.split( ',' ) ] + variants = [ v.strip() for v in options.variants.split( ',' ) ] + variant_exclusions = {} + try: + for ve in options.variant_exclusions.split( ';' ): + v, e = ve.split( ':' ) + variant_exclusions[ v ] = e.split( ',' ) + except: + sys.stderr.write( 'Problem parsing the variant exclusion parameter (-n/--variant-exclusion). Make sure it follows the expected format\n' ) + sys.exit( 1 ) + if options.append: + sample_text = False + else: + sample_text = options.sample_text + + # all paths to look in + if options.inspect_dir: + paths_to_look_in = [ os.path.join( options.genome_dir, '%s', id ) for id in options.inspect_dir.split( ',' ) ] + else: + paths_to_look_in = os.path.join( options.genome_dir, '%s' ) + + # say what we're looking in + print '\nLooking in:\n\t%s' % '\n\t'.join( [ p % '<build_name>' for p in paths_to_look_in ] ) + poss_names = [ '<build_name>%s' % v for v in variants ] + print 'for files that are named %s' % ', '.join( poss_names[:-1] ), + if len( poss_names ) > 1: + print 'or %s' % poss_names[-1], + if len( options.fasta_exts ) == 1: + print 'with the extension %s.' % ', '.join( fasta_exts[:-1] ) + else: + print 'with the extension %s or %s.' % ( ', '.join( fasta_exts[:-1] ), fasta_exts[-1] ) + print '\nSkipping the following:\n\t%s' % '\n\t'.join( exemptions ) + + # get column names + col_values = [] + loc_path = None + tree = etree.parse( options.data_table_xml ) + tables = tree.getroot() + for table in tables.getiterator(): + name = table.attrib.get( 'name' ) + if name == options.data_table_name: + cols = None + for node in table.getiterator(): + if node.tag == 'columns': + cols = node.text + elif node.tag == 'file': + loc_path = node.attrib.get( 'path' ) + if cols: + col_values = [ col.strip() for col in cols.split( ',' ) ] + if not col_values or not loc_path: + stop_err( 'No columns can be found for this data table (%s) in %s' % ( options.data_table, options.data_table_xml ) ) + + # get all fasta paths under genome directory + fasta_locs = {} + unmatching_fasta_paths = [] + genome_subdirs = [ dr for dr in os.listdir( options.genome_dir ) if dr not in exemptions ] + for genome_subdir in genome_subdirs: + possible_names = [ genome_subdir ] + possible_names.extend( [ '%s%s' % ( genome_subdir, v ) for v in variants ] ) + # get paths to all fasta files + for path_to_look_in in paths_to_look_in: + for dirpath, dirnames, filenames in os.walk( path_to_look_in % genome_subdir ): + for fn in filenames: + ext = os.path.splitext( fn )[-1] + fasta_base = os.path.splitext( fn )[0] + if ext in fasta_exts: + if fasta_base in possible_names: + if fasta_base == genome_subdir: + name = DBKEY_DESCRIPTION_MAP[ genome_subdir ] + else: + try: + name = '%s %s' % ( DBKEY_DESCRIPTION_MAP[ genome_subdir ], VARIANT_MAP[ fasta_base.replace( genome_subdir, '' ) ] ) + except KeyError: + name = '%s %s' % ( DBKEY_DESCRIPTION_MAP[ genome_subdir ], fasta_base.replace( genome_subdir, '' ) ) + fasta_locs[ fasta_base ] = { 'value': fasta_base, 'dbkey': genome_subdir, 'name': name, 'path': os.path.join( dirpath, fn ) } + else: + unmatching_fasta_paths.append( os.path.join( dirpath, fn ) ) + # remove redundant fasta files + if variant_exclusions.keys(): + for k in variant_exclusions.keys(): + leave_in = '%s%s' % ( genome_subdir, k ) + if fasta_locs.has_key( leave_in ): + to_remove = [ '%s%s' % ( genome_subdir, k ) for k in variant_exclusions[ k ] ] + for tr in to_remove: + if fasta_locs.has_key( tr ): + del fasta_locs[ tr ] + + # output results + print '\nThere were %s fasta files found that were not included because they did not have the expected file names.' % len( unmatching_fasta_paths ) + print '%s fasta files were found and listed.\n' % len( fasta_locs.keys() ) + + # output unmatching fasta files + if options.unmatching_fasta and unmatching_fasta_paths: + open( options.unmatching_fasta, 'wb' ).write( '%s\n' % '\n'.join( unmatching_fasta_paths ) ) + + # output loc file + if options.append: + all_fasta_loc = open( loc_path, 'ab' ) + else: + all_fasta_loc = open( loc_path, 'wb' ) + # put sample loc file text at top of file if appropriate + if sample_text: + if options.loc_sample_name: + all_fasta_loc.write( '%s\n' % open( options.loc_sample_name, 'rb' ).read().strip() ) + else: + all_fasta_loc.write( '%s\n' % open( '%s.sample' % loc_path, 'rb' ).read().strip() ) + # output list of fasta files in alphabetical order + fasta_bases = fasta_locs.keys() + fasta_bases.sort( caseless_compare ) + for fb in fasta_bases: + out_line = [] + for col in col_values: + try: + out_line.append( fasta_locs[ fb ][ col ] ) + except KeyError: + stop_err( 'Unexpected column (%s) encountered' % col ) + if out_line: + all_fasta_loc.write( '%s\n' % '\t'.join( out_line ) ) + # close up output loc file + all_fasta_loc.close() + +if __name__=='__main__': __main__()