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()
