def main(argv=None): if argv is None: argv = sys.argv parser = E.OptionParser(version="%prog version: $Id$", usage=globals()["__doc__"]) parser.add_option( "-e", "--extract", dest="extract", type="string", help="extract region for testing purposes. Format is " "contig:strand:from:to. " "The default coordinates are 0-based " "open/closed coordinates on both strands, but can be changed " "by --input-format. " "For example, 'chr1:+:10:12' will return " "bases 11 and 12 on chr1. Elements from the end of the " "string can be omitted. For example, 'chr1' will return " "all of chromosome 'chr1'.") input_format_choices = ("one-forward-open", "zero-both-open") parser.add_option("-i", "--input-format", dest="input_format", type="choice", choices=input_format_choices, help="coordinate format of input. Valid choices are " "%s. See --extract. [default=%%default]." % ", ".join(input_format_choices)) parser.add_option( "-s", "--synonyms", dest="synonyms", type="string", help="list of synonyms. This is a comma separated with list " "of equivalence relations. For example, chrM=chrMT " "means that chrMT will refer to chrM and either " "can be used to retrieve a sequence " "[default=%default]") group = E.OptionGroup(parser, "Bencharking options") group.add_option("-b", "--benchmark", dest="benchmark", action="store_true", help="benchmark time for read access " "[default=%default].") group.add_option("--benchmark-num-iterations", dest="benchmark_num_iterations", type="int", help="number of iterations for benchmark " "[default=%default].") group.add_option("--benchmark-fragment-size", dest="benchmark_fragment_size", type="int", help="benchmark: fragment size [default=%default].") parser.add_option_group(group) group = E.OptionGroup(parser, "Validation options") group.add_option("--verify", dest="verify", type="string", help="verify against other database [default=%default].") group.add_option("--verify-iterations", dest="verify_num_iterations", type="int", help="number of iterations for verification " "[default=%default].") parser.add_option_group(group) file_format_choices = ("fasta", "auto", "fasta.gz", "tar", "tar.gz") parser.add_option("--file-format", dest="file_format", type="choice", choices=file_format_choices, help="file format of input. Supply if data comes " "from stdin " "Valid choices are %s [default=%%default]." % ", ".join(file_format_choices)) parser.add_option("-a", "--clean-sequence", dest="clean_sequence", action="store_true", help="remove X/x from DNA sequences - they cause " "errors in exonerate [default=%default].") parser.add_option("--allow-duplicates", dest="allow_duplicates", action="store_true", help="allow duplicate identifiers. Further occurances " "of an identifier are suffixed by an '_%i' " "[default=%default].") parser.add_option("--regex-identifier", dest="regex_identifier", type="string", help="regular expression for extracting the " "identifier from fasta description line " "[default=%default].") parser.add_option("--force-output", dest="force", action="store_true", help="force overwriting of existing files " "[default=%default].") translator_choices = ("solexa", "phred", "bytes", "range200") parser.add_option("-t", "--translator", dest="translator", type="choice", choices=translator_choices, help="translate numerical quality scores. " "Valid choices are %s [default=%%default]." % ", ".join(translator_choices)) group = E.OptionGroup(parser, 'Compression options') compression_choices = ("lzo", "zlib", "gzip", "dictzip", "bzip2", "debug") group.add_option("-c", "--compression", dest="compression", type="choice", choices=compression_choices, help="compress database, using specified compression " "method. " "Valid choices are %s, but depend on availability on the " "system " "[default=%%default]." % ", ".join(compression_choices)) group.add_option("--random-access-points", dest="random_access_points", type="int", help="set random access points every # number " "of nucleotides for block compression schemes " "[default=%default].") group.add_option( "--compress-index", dest="compress_index", action="store_true", help="compress index. The default is to use a plain-text, " "human-readable index [default=%default].") parser.add_option_group(group) parser.set_defaults(extract=None, input_format="zero-both-open", benchmark_fragment_size=1000, benchmark_num_iterations=1000000, benchmark=False, compression=None, random_access_points=0, synonyms=None, verify=None, verify_num_iterations=100000, verify_fragment_size=100, clean_sequence=False, allow_duplicates=False, regex_identifier=None, compress_index=False, file_format="auto", force=False, translator=None) (options, args) = E.Start(parser) if options.synonyms: synonyms = {} for x in options.synonyms.split(","): a, b = x.split("=") a = a.strip() b = b.strip() if a not in synonyms: synonyms[a] = [] synonyms[a].append(b) else: synonyms = None if options.translator: if options.translator == "phred": options.translator = IndexedFasta.TranslatorPhred() elif options.translator == "solexa": options.translator = IndexedFasta.TranslatorSolexa() elif options.translator == "bytes": options.translator = IndexedFasta.TranslatorBytes() elif options.translator == "range200": options.translator = IndexedFasta.TranslatorRange200() else: raise ValueError("unknown translator %s" % options.translator) if options.extract: fasta = IndexedFasta.IndexedFasta(args[0]) fasta.setTranslator(options.translator) converter = IndexedFasta.getConverter(options.input_format) contig, strand, start, end = IndexedFasta.parseCoordinates( options.extract) sequence = fasta.getSequence(contig, strand, start, end, converter=converter) options.stdout.write(">%s\n%s\n" % (options.extract, sequence)) elif options.benchmark: import timeit timer = timeit.Timer( stmt="IndexedFasta.benchmarkRandomFragment(fasta=fasta, size=%i)" % (options.benchmark_fragment_size), setup="from __main__ import IndexedFasta\n" "fasta=IndexedFasta.IndexedFasta('%s')" % (args[0])) t = timer.timeit(number=options.benchmark_num_iterations) options.stdout.write("iter\tsize\ttime\n") options.stdout.write("%i\t%i\t%i\n" % (options.benchmark_num_iterations, options.benchmark_fragment_size, t)) elif options.verify: fasta1 = IndexedFasta.IndexedFasta(args[0]) fasta2 = IndexedFasta.IndexedFasta(options.verify) nerrors1 = IndexedFasta.verify(fasta1, fasta2, options.verify_num_iterations, options.verify_fragment_size, stdout=options.stdout) options.stdout.write("errors=%i\n" % (nerrors1)) nerrors2 = IndexedFasta.verify(fasta2, fasta1, options.verify_num_iterations, options.verify_fragment_size, stdout=options.stdout) options.stdout.write("errors=%i\n" % (nerrors2)) elif options.compress_index: fasta = IndexedFasta.IndexedFasta(args[0]) fasta.compressIndex() else: if options.loglevel >= 1: options.stdlog.write("# creating database %s\n" % args[0]) options.stdlog.write("# indexing the following files: \n# %s\n" % (" \n# ".join(args[1:]))) options.stdlog.flush() if synonyms: options.stdlog.write("# Applying the following synonyms:\n") for k, v in synonyms.items(): options.stdlog.write("# %s=%s\n" % (k, ",".join(v))) options.stdlog.flush() if len(args) < 2: print globals()["__doc__"] sys.exit(1) iterator = IndexedFasta.MultipleFastaIterator( args[1:], regex_identifier=options.regex_identifier, format=options.file_format) IndexedFasta.createDatabase( args[0], iterator, synonyms=synonyms, random_access_points=options.random_access_points, compression=options.compression, clean_sequence=options.clean_sequence, allow_duplicates=options.allow_duplicates, translator=options.translator, force=options.force) E.Stop()
def main(argv=None): if argv == None: argv = sys.argv parser = E.OptionParser( version= "%prog version: $Id: IndexedFasta.py 2801 2009-10-22 13:40:39Z andreas $", usage=globals()["__doc__"]) parser.add_option( "-e", "--extract", dest="extract", type="string", help= "extract region for testing purposes. Format is contig:strand:from:to. " "The default coordinates are 0-based open/closed coordinates on both strands. " "For example, chr1:+:10:12 will return bases 11 to 12 on chr1.") parser.add_option("-c", "--compression", dest="compression", type="choice", choices=("lzo", "zlib", "gzip", "dictzip", "bzip2", "debug"), help="compress database [default=%default].") parser.add_option( "--random-access-points", dest="random_access_points", type="int", help= "save random access points every # number of nucleotides [default=%default]." ) parser.add_option("-i", "--input-format", dest="input_format", type="choice", choices=("one-forward-open", "zero-both-open"), help="coordinate format of input [default=%default].") parser.add_option( "-s", "--synonyms", dest="synonyms", type="string", help= "list of synonyms, comma separated with =, for example, chr1=chr1b [default=%default]" ) parser.add_option( "-b", "--benchmark", dest="benchmark", action="store_true", help="benchmark time for read access [default=%default].") parser.add_option( "--benchmark-num-iterations", dest="benchmark_num_iterations", type="int", help="number of iterations for benchmark [default=%default].") parser.add_option("--benchmark-fragment-size", dest="benchmark_fragment_size", type="int", help="benchmark: fragment size [default=%default].") parser.add_option("--verify", dest="verify", type="string", help="verify against other database [default=%default].") parser.add_option( "--file-format", dest="file_format", type="choice", choices=("fasta", "auto", "fasta.gz", "tar", "tar.gz"), help= "file format of input. Supply if data comes from stdin [default=%default]." ) parser.add_option( "-a", "--clean-sequence", dest="clean_sequence", action="store_true", help= "remove X/x from DNA sequences - they cause errors in exonerate [default=%default]." ) parser.add_option( "--allow-duplicates", dest="allow_duplicates", action="store_true", help= "allow duplicate identifiers. Further occurances of an identifier are suffixed by an '_%i' [default=%default]." ) parser.add_option( "--regex-identifier", dest="regex_identifier", type="string", help= "regular expression for extracting the identifier from fasta description line [default=%default]." ) parser.add_option("--compress-index", dest="compress_index", action="store_true", help="compress index [default=%default].") parser.add_option( "--force", dest="force", action="store_true", help="force overwriting of existing files [default=%default].") parser.add_option( "-t", "--translator", dest="translator", type="choice", choices=("solexa", "phred", "bytes", "range200"), help="translate numerical quality scores [default=%default].") parser.set_defaults(extract=None, input_format="zero-both-open", benchmark_fragment_size=1000, benchmark_num_iterations=1000000, benchmark=False, compression=None, random_access_points=0, synonyms=None, verify=None, verify_num_iterations=100000, verify_fragment_size=100, clean_sequence=False, allow_duplicates=False, regex_identifier=None, compress_index=False, file_format="auto", force=False, translator=None) (options, args) = E.Start(parser) if options.synonyms: synonyms = {} for x in options.synonyms.split(","): a, b = x.split("=") a = a.strip() b = b.strip() if a not in synonyms: synonyms[a] = [] synonyms[a].append(b) else: synonyms = None if options.translator: if options.translator == "phred": options.translator = TranslatorPhred() elif options.translator == "solexa": options.translator = TranslatorSolexa() elif options.translator == "bytes": options.translator = TranslatorBytes() elif options.translator == "range200": options.translator = TranslatorRange200() else: raise ValueError("unknown translator %s" % options.translator) if options.extract: fasta = IndexedFasta.IndexedFasta(args[0]) fasta.setTranslator(options.translator) converter = IndexedFasta.getConverter(options.input_format) contig, strand, start, end = IndexedFasta.parseCoordinates( options.extract) sequence = fasta.getSequence(contig, strand, start, end, converter=converter) options.stdout.write( ">%s\n%s\n" % \ ( options.extract, sequence ) ) elif options.benchmark: import timeit timer = timeit.Timer( stmt="benchmarkRandomFragment( fasta = fasta, size = %i)" % (options.benchmark_fragment_size), setup= """from __main__ import benchmarkRandomFragment,IndexedFasta\nfasta=IndexedFasta.IndexedFasta( "%s" )""" % (args[0])) t = timer.timeit(number=options.benchmark_num_iterations) options.stdout.write("iter\tsize\ttime\n") options.stdout.write("%i\t%i\t%i\n" % (options.benchmark_num_iterations, options.benchmark_fragment_size, t)) elif options.verify: fasta1 = IndexedFasta.IndexedFasta(args[0]) fasta2 = IndexedFasta.IndexedFasta(options.verify) nerrors1 = verify(fasta1, fasta2, options.verify_num_iterations, options.verify_fragment_size, stdout=options.stdout) options.stdout.write("errors=%i\n" % (nerrors1)) nerrors2 = IndexedFasta.verify(fasta2, fasta1, options.verify_num_iterations, options.verify_fragment_size, stdout=options.stdout) options.stdout.write("errors=%i\n" % (nerrors2)) elif options.compress_index: fasta = IndexedFasta.IndexedFasta(args[0]) fasta.compressIndex() else: if options.loglevel >= 1: options.stdlog.write("# creating database %s\n" % args[0]) options.stdlog.write("# indexing the following files: \n# %s\n" %\ (" \n# ".join( args[1:] ) )) options.stdlog.flush() if synonyms: options.stdlog.write("# Applying the following synonyms:\n") for k, v in synonyms.items(): options.stdlog.write("# %s=%s\n" % (k, ",".join(v))) options.stdlog.flush() if len(args) < 2: print globals()["__doc__"] sys.exit(1) iterator = IndexedFasta.MultipleFastaIterator( args[1:], regex_identifier=options.regex_identifier, format=options.file_format) IndexedFasta.createDatabase( args[0], iterator, synonyms=synonyms, random_access_points=options.random_access_points, compression=options.compression, clean_sequence=options.clean_sequence, allow_duplicates=options.allow_duplicates, translator=options.translator, force=options.force) E.Stop()
def main(argv=None): if argv is None: argv = sys.argv parser = E.OptionParser(version="%prog version: $Id$", usage=globals()["__doc__"]) parser.add_option("-e", "--extract", dest="extract", type="string", help="extract region for testing purposes. Format is " "contig:strand:from:to. " "The default coordinates are 0-based " "open/closed coordinates on both strands. " "For example, chr1:+:10:12 will return " "bases 11 to 12 on chr1.") compression_choices = ("lzo", "zlib", "gzip", "dictzip", "bzip2", "debug") parser.add_option("-c", "--compression", dest="compression", type="choice", choices=compression_choices, help="compress database, using specied compression. " "Valid choices are %s. " "[default=%%default]." % ", ".join(compression_choices)) parser.add_option("--random-access-points", dest="random_access_points", type="int", help="save random access points every # number " "of nucleotides [default=%default].") input_format_choices = ("one-forward-open", "zero-both-open") parser.add_option("-i", "--input-format", dest="input_format", type="choice", choices=input_format_choices, help="coordinate format of input. Valid choices are " "%s [default=%%default]." % ", ".join(input_format_choices)) parser.add_option("-s", "--synonyms", dest="synonyms", type="string", help="list of synonyms, comma separated with =, " "for example, chr1=chr1b [default=%default]") parser.add_option("-b", "--benchmark", dest="benchmark", action="store_true", help="benchmark time for read access " "[default=%default].") parser.add_option("--benchmark-num-iterations", dest="benchmark_num_iterations", type="int", help="number of iterations for benchmark " "[default=%default].") parser.add_option("--benchmark-fragment-size", dest="benchmark_fragment_size", type="int", help="benchmark: fragment size [default=%default].") parser.add_option("--verify", dest="verify", type="string", help="verify against other database [default=%default].") parser.add_option("--verify-iterations", dest="verify_num_iterations", type="int", help="number of iterations for verification " "[default=%default].") file_format_choices = ("fasta", "auto", "fasta.gz", "tar", "tar.gz") parser.add_option("--file-format", dest="file_format", type="choice", choices=file_format_choices, help="file format of input. Supply if data comes " "from stdin " "Valid choices are %s [default=%%default]." % ", ".join(file_format_choices)) parser.add_option("-a", "--clean-sequence", dest="clean_sequence", action="store_true", help="remove X/x from DNA sequences - they cause " "errors in exonerate [default=%default].") parser.add_option("--allow-duplicates", dest="allow_duplicates", action="store_true", help="allow duplicate identifiers. Further occurances " "of an identifier are suffixed by an '_%i' " "[default=%default].") parser.add_option("--regex-identifier", dest="regex_identifier", type="string", help="regular expression for extracting the " "identifier from fasta description line " "[default=%default].") parser.add_option("--compress-index", dest="compress_index", action="store_true", help="compress index [default=%default].") parser.add_option("--force", dest="force", action="store_true", help="force overwriting of existing files " "[default=%default].") translator_choices = ("solexa", "phred", "bytes", "range200") parser.add_option("-t", "--translator", dest="translator", type="choice", choices=translator_choices, help="translate numerical quality scores. " "Valid choices are %s [default=%%default]." % ", ".join(translator_choices)) parser.set_defaults( extract=None, input_format="zero-both-open", benchmark_fragment_size=1000, benchmark_num_iterations=1000000, benchmark=False, compression=None, random_access_points=0, synonyms=None, verify=None, verify_num_iterations=100000, verify_fragment_size=100, clean_sequence=False, allow_duplicates=False, regex_identifier=None, compress_index=False, file_format="auto", force=False, translator=None) (options, args) = E.Start(parser) if options.synonyms: synonyms = {} for x in options.synonyms.split(","): a, b = x.split("=") a = a.strip() b = b.strip() if a not in synonyms: synonyms[a] = [] synonyms[a].append(b) else: synonyms = None if options.translator: if options.translator == "phred": options.translator = IndexedFasta.TranslatorPhred() elif options.translator == "solexa": options.translator = IndexedFasta.TranslatorSolexa() elif options.translator == "bytes": options.translator = IndexedFasta.TranslatorBytes() elif options.translator == "range200": options.translator = IndexedFasta.TranslatorRange200() else: raise ValueError("unknown translator %s" % options.translator) if options.extract: fasta = IndexedFasta.IndexedFasta(args[0]) fasta.setTranslator(options.translator) converter = IndexedFasta.getConverter(options.input_format) contig, strand, start, end = IndexedFasta.parseCoordinates( options.extract) sequence = fasta.getSequence(contig, strand, start, end, converter=converter) options.stdout.write(">%s\n%s\n" % (options.extract, sequence)) elif options.benchmark: import timeit timer = timeit.Timer( stmt="IndexedFasta.benchmarkRandomFragment( fasta = fasta, size = %i)" % ( options.benchmark_fragment_size), setup="""from __main__ import IndexedFasta\nfasta=IndexedFasta.IndexedFasta( "%s" )""" % (args[0] ) ) t = timer.timeit(number=options.benchmark_num_iterations) options.stdout.write("iter\tsize\ttime\n") options.stdout.write("%i\t%i\t%i\n" % ( options.benchmark_num_iterations, options.benchmark_fragment_size, t)) elif options.verify: fasta1 = IndexedFasta.IndexedFasta(args[0]) fasta2 = IndexedFasta.IndexedFasta(options.verify) nerrors1 = IndexedFasta.verify(fasta1, fasta2, options.verify_num_iterations, options.verify_fragment_size, stdout=options.stdout) options.stdout.write("errors=%i\n" % (nerrors1)) nerrors2 = IndexedFasta.verify(fasta2, fasta1, options.verify_num_iterations, options.verify_fragment_size, stdout=options.stdout) options.stdout.write("errors=%i\n" % (nerrors2)) elif options.compress_index: fasta = IndexedFasta.IndexedFasta(args[0]) fasta.compressIndex() else: if options.loglevel >= 1: options.stdlog.write("# creating database %s\n" % args[0]) options.stdlog.write("# indexing the following files: \n# %s\n" % (" \n# ".join(args[1:]))) options.stdlog.flush() if synonyms: options.stdlog.write("# Applying the following synonyms:\n") for k, v in synonyms.items(): options.stdlog.write("# %s=%s\n" % (k, ",".join(v))) options.stdlog.flush() if len(args) < 2: print globals()["__doc__"] sys.exit(1) iterator = IndexedFasta.MultipleFastaIterator( args[1:], regex_identifier=options.regex_identifier, format=options.file_format) IndexedFasta.createDatabase( args[0], iterator, synonyms=synonyms, random_access_points=options.random_access_points, compression=options.compression, clean_sequence=options.clean_sequence, allow_duplicates=options.allow_duplicates, translator=options.translator, force=options.force) E.Stop()