def main(argv=None):
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-g", "--genome-file", dest="genome_file", type="string",
help="filename with genomic sequence to retrieve "
"sequences from.")
parser.add_option("-m", "--masker", dest="masker", type="choice",
choices=("dust", "dustmasker", "softmask", "none"),
help="apply masker to mask output sequences "
"[%default].")
parser.add_option("--output-mode", dest="output_mode", type="choice",
choices=("intervals", "leftright", "segments"),
help="what to output. "
"'intervals' generates a single sequence for "
"each bed interval. 'leftright' generates two "
"sequences, one in each direction, for each bed "
"interval. 'segments' can be used to output "
"sequence from bed12 files so that sequence only covers "
"the segements [%default]")
parser.add_option("--min-sequence-length", dest="min_length", type="int",
help="require a minimum sequence length [%default]")
parser.add_option("--max-sequence-length", dest="max_length", type="int",
help="require a maximum sequence length [%default]")
parser.add_option(
"--extend-at", dest="extend_at", type="choice",
choices=("none", "3", "5", "both", "3only", "5only"),
help="extend at 3', 5' or both or no ends. If 3only or 5only "
"are set, only the added sequence is returned [default=%default]")
parser.add_option(
"--extend-by", dest="extend_by", type="int",
help="extend by # bases [default=%default]")
parser.add_option(
"--use-strand", dest="ignore_strand",
action="store_false",
help="use strand information and return reverse complement "
"on intervals located on the negative strand. "
"[default=%default]")
parser.set_defaults(
genome_file=None,
masker=None,
output_mode="intervals",
min_length=0,
max_length=0,
extend_at=None,
extend_by=100,
ignore_strand=True,
)
(options, args) = E.start(parser)
if options.genome_file:
fasta = IndexedFasta.IndexedFasta(options.genome_file)
contigs = fasta.getContigSizes()
fasta.setConverter(IndexedFasta.getConverter("zero-both-open"))
counter = E.Counter()
ids, seqs = [], []
E.info("collecting sequences")
for bed in Bed.setName(Bed.iterator(options.stdin)):
counter.input += 1
lcontig = fasta.getLength(bed.contig)
if options.ignore_strand:
strand = "+"
else:
strand = bed.strand
if options.output_mode == "segments" and bed.columns == 12:
ids.append("%s %s:%i..%i (%s) %s %s" %
(bed.name, bed.contig, bed.start, bed.end, strand,
bed["blockSizes"], bed["blockStarts"]))
seg_seqs = [fasta.getSequence(bed.contig, strand, start, end)
for start, end in bed.toIntervals()]
seqs.append("".join(seg_seqs))
elif (options.output_mode == "intervals" or
options.output_mode == "segments"):
ids.append("%s %s:%i..%i (%s)" %
(bed.name, bed.contig, bed.start, bed.end, strand))
seqs.append(
fasta.getSequence(bed.contig, strand, bed.start, bed.end))
elif options.output_mode == "leftright":
l = bed.end - bed.start
start, end = max(0, bed.start - l), bed.end - l
ids.append("%s_l %s:%i..%i (%s)" %
(bed.name, bed.contig, start, end, strand))
seqs.append(fasta.getSequence(bed.contig, strand, start, end))
start, end = bed.start + l, min(lcontig, bed.end + l)
ids.append("%s_r %s:%i..%i (%s)" %
(bed.name, bed.contig, start, end, strand))
seqs.append(fasta.getSequence(bed.contig, strand, start, end))
E.info("collected %i sequences" % len(seqs))
masked = Masker.maskSequences(seqs, options.masker)
options.stdout.write(
"\n".join([">%s\n%s" % (x, y) for x, y in zip(ids, masked)]) + "\n")
E.info("masked %i sequences" % len(seqs))
counter.output = len(seqs)
E.info("%s" % counter)
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, 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 cgat 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 list(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()