def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("--is-gtf",
dest="is_gtf",
action="store_true",
help="input is gtf instead of gff.")
parser.add_option("-g",
"--genome-file",
dest="genome_file",
type="string",
help="filename with genome [default=%default].")
parser.add_option("-m",
"--merge-adjacent",
dest="merge",
action="store_true",
help="merge adjacent intervals with the same attributes."
" [default=%default]")
parser.add_option("-e",
"--feature",
dest="feature",
type="string",
help="filter by a feature, for example 'exon', 'CDS'."
" If set to the empty string, all entries are output "
"[%default].")
parser.add_option("-f",
"--maskregions-bed-file",
dest="filename_masks",
type="string",
metavar="gff",
help="mask sequences with regions given in gff file "
"[%default].")
parser.add_option("--remove-masked-regions",
dest="remove_masked_regions",
action="store_true",
help="remove regions instead of masking [%default].")
parser.add_option("--min-interval-length",
dest="min_length",
type="int",
help="set minimum length for sequences output "
"[%default]")
parser.add_option("--max-length",
dest="max_length",
type="int",
help="set maximum length for sequences output "
"[%default]")
parser.add_option("--extend-at",
dest="extend_at",
type="choice",
choices=("none", "3", "5", "both", "3only", "5only"),
help="extend at no end, 3', 5' or both 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("--extend-with",
dest="extend_with",
type="string",
help="extend using base [default=%default]")
parser.add_option("--masker",
dest="masker",
type="choice",
choices=("dust", "dustmasker", "softmask", "none"),
help="apply masker [%default].")
parser.add_option("--fold-at",
dest="fold_at",
type="int",
help="fold sequence every n bases[%default].")
parser.add_option(
"--fasta-name-attribute",
dest="naming_attribute",
type="string",
help="use attribute to name fasta entry. Currently only compatable"
" with gff format [%default].")
parser.set_defaults(is_gtf=False,
genome_file=None,
merge=False,
feature=None,
filename_masks=None,
remove_masked_regions=False,
min_length=0,
max_length=0,
extend_at=None,
extend_by=100,
extend_with=None,
masker=None,
fold_at=None,
naming_attribute=False)
(options, args) = E.Start(parser)
if options.genome_file:
fasta = IndexedFasta.IndexedFasta(options.genome_file)
contigs = fasta.getContigSizes()
if options.is_gtf:
iterator = GTF.transcript_iterator(GTF.iterator(options.stdin))
else:
gffs = GTF.iterator(options.stdin)
if options.merge:
iterator = GTF.joined_iterator(gffs)
else:
iterator = GTF.chunk_iterator(gffs)
masks = None
if options.filename_masks:
masks = {}
with IOTools.openFile(options.filename_masks, "r") as infile:
e = GTF.readAsIntervals(GTF.iterator(infile))
# convert intervals to intersectors
for contig in list(e.keys()):
intersector = bx.intervals.intersection.Intersecter()
for start, end in e[contig]:
intersector.add_interval(bx.intervals.Interval(start, end))
masks[contig] = intersector
ninput, noutput, nmasked, nskipped_masked = 0, 0, 0, 0
nskipped_length = 0
nskipped_noexons = 0
feature = options.feature
# iterator is a list containing groups (lists) of features.
# Each group of features have in common the same transcript ID, in case of
# GTF files.
for ichunk in iterator:
ninput += 1
if feature:
chunk = [x for x in ichunk if x.feature == feature]
else:
chunk = ichunk
if len(chunk) == 0:
nskipped_noexons += 1
E.info("no features in entry from "
"%s:%i..%i - %s" % (ichunk[0].contig, ichunk[0].start,
ichunk[0].end, str(ichunk[0])))
continue
contig, strand = chunk[0].contig, chunk[0].strand
if options.is_gtf:
name = chunk[0].transcript_id
else:
if options.naming_attribute:
attr_dict = {
x.split("=")[0]: x.split("=")[1]
for x in chunk[0].attributes.split(";")
}
name = attr_dict[options.naming_attribute]
else:
name = str(chunk[0].attributes)
lcontig = contigs[contig]
positive = Genomics.IsPositiveStrand(strand)
intervals = [(x.start, x.end) for x in chunk]
intervals.sort()
if masks:
if contig in masks:
masked_regions = []
for start, end in intervals:
masked_regions += [(x.start, x.end)
for x in masks[contig].find(start, end)]
masked_regions = Intervals.combine(masked_regions)
if len(masked_regions):
nmasked += 1
if options.remove_masked_regions:
intervals = Intervals.truncate(intervals, masked_regions)
else:
raise NotImplementedError("unimplemented")
if len(intervals) == 0:
nskipped_masked += 1
if options.loglevel >= 1:
options.stdlog.write(
"# skipped because fully masked: "
"%s: regions=%s masks=%s\n" %
(name, str([(x.start, x.end)
for x in chunk]), masked_regions))
continue
out = intervals
if options.extend_at and not options.extend_with:
if options.extend_at == "5only":
intervals = [(max(0, intervals[0][0] - options.extend_by),
intervals[0][0])]
elif options.extend_at == "3only":
intervals = [(intervals[-1][1],
min(lcontig,
intervals[-1][1] + options.extend_by))]
else:
if options.extend_at in ("5", "both"):
intervals[0] = (max(0,
intervals[0][0] - options.extend_by),
intervals[0][1])
if options.extend_at in ("3", "both"):
intervals[-1] = (intervals[-1][0],
min(lcontig,
intervals[-1][1] + options.extend_by))
if not positive:
intervals = [(lcontig - x[1], lcontig - x[0])
for x in intervals[::-1]]
out.reverse()
s = [
fasta.getSequence(contig, strand, start, end)
for start, end in intervals
]
# IMS: allow for masking of sequences
s = Masker.maskSequences(s, options.masker)
l = sum([len(x) for x in s])
if (l < options.min_length
or (options.max_length and l > options.max_length)):
nskipped_length += 1
if options.loglevel >= 1:
options.stdlog.write("# skipped because length out of bounds "
"%s: regions=%s len=%i\n" %
(name, str(intervals), l))
continue
if options.extend_at and options.extend_with:
extension = "".join((options.extend_with, ) * options.extend_by)
if options.extend_at in ("5", "both"):
s[1] = extension + s[1]
if options.extend_at in ("3", "both"):
s[-1] = s[-1] + extension
if options.fold_at:
n = options.fold_at
s = "".join(s)
seq = "\n".join([s[i:i + n] for i in range(0, len(s), n)])
else:
seq = "\n".join(s)
options.stdout.write(
">%s %s:%s:%s\n%s\n" %
(name, contig, strand, ";".join(["%i-%i" % x for x in out]), seq))
noutput += 1
E.info("ninput=%i, noutput=%i, nmasked=%i, nskipped_noexons=%i, "
"nskipped_masked=%i, nskipped_length=%i" %
(ninput, noutput, nmasked, nskipped_noexons, nskipped_masked,
nskipped_length))
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("-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):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("--is-gtf", dest="is_gtf", action="store_true",
help="input is gtf instead of gff.")
parser.add_option("-g", "--genome-file", dest="genome_file", type="string",
help="filename with genome [default=%default].")
parser.add_option(
"-m", "--merge-adjacent", dest="merge", action="store_true",
help="merge adjacent intervals with the same attributes."
" [default=%default]")
parser.add_option(
"-e", "--feature", dest="feature", type="string",
help="filter by a feature, for example 'exon', 'CDS'."
" If set to the empty string, all entries are output "
"[%default].")
parser.add_option(
"-f", "--maskregions-bed-file", dest="filename_masks",
type="string", metavar="gff",
help="mask sequences with regions given in gff file "
"[%default].")
parser.add_option(
"--remove-masked-regions", dest="remove_masked_regions",
action="store_true",
help="remove regions instead of masking [%default].")
parser.add_option(
"--min-interval-length", dest="min_length", type="int",
help="set minimum length for sequences output "
"[%default]")
parser.add_option(
"--max-length", dest="max_length", type="int",
help="set maximum length for sequences output "
"[%default]")
parser.add_option(
"--extend-at", dest="extend_at", type="choice",
choices=("none", "3", "5", "both", "3only", "5only"),
help="extend at no end, 3', 5' or both 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(
"--extend-with", dest="extend_with", type="string",
help="extend using base [default=%default]")
parser.add_option(
"--masker", dest="masker", type="choice",
choices=("dust", "dustmasker", "softmask", "none"),
help="apply masker [%default].")
parser.add_option(
"--fold-at", dest="fold_at", type="int",
help="fold sequence every n bases[%default].")
parser.add_option(
"--fasta-name-attribute", dest="naming_attribute", type="string",
help="use attribute to name fasta entry. Currently only compatable"
" with gff format [%default].")
parser.set_defaults(
is_gtf=False,
genome_file=None,
merge=False,
feature=None,
filename_masks=None,
remove_masked_regions=False,
min_length=0,
max_length=0,
extend_at=None,
extend_by=100,
extend_with=None,
masker=None,
fold_at=None,
naming_attribute=False
)
(options, args) = E.Start(parser)
if options.genome_file:
fasta = IndexedFasta.IndexedFasta(options.genome_file)
contigs = fasta.getContigSizes()
if options.is_gtf:
iterator = GTF.transcript_iterator(GTF.iterator(options.stdin))
else:
gffs = GTF.iterator(options.stdin)
if options.merge:
iterator = GTF.joined_iterator(gffs)
else:
iterator = GTF.chunk_iterator(gffs)
masks = None
if options.filename_masks:
masks = {}
with open(options.filename_masks, "r") as infile:
e = GTF.readAsIntervals(GTF.iterator(infile))
# convert intervals to intersectors
for contig in e.keys():
intersector = bx.intervals.intersection.Intersecter()
for start, end in e[contig]:
intersector.add_interval(bx.intervals.Interval(start, end))
masks[contig] = intersector
ninput, noutput, nmasked, nskipped_masked = 0, 0, 0, 0
nskipped_length = 0
nskipped_noexons = 0
feature = options.feature
# for item in iterator:
# print len(item) # 3, 2
# for i in item:
# print len(i) # 9, 9, 9, 9, 9
# print i.contig
# print i.strand
# print i.transcript_id
# iterator is a list containing groups (lists) of features.
# Each group of features have in common the same transcript ID, in case of
# GTF files.
for ichunk in iterator:
ninput += 1
if feature:
chunk = filter(lambda x: x.feature == feature, ichunk)
else:
chunk = ichunk
if len(chunk) == 0:
nskipped_noexons += 1
E.info("no features in entry from "
"%s:%i..%i - %s" % (ichunk[0].contig,
ichunk[0].start,
ichunk[0].end,
str(ichunk[0])))
continue
contig, strand = chunk[0].contig, chunk[0].strand
if options.is_gtf:
name = chunk[0].transcript_id
else:
if options.naming_attribute:
attr_dict = {x.split("=")[0]: x.split("=")[1]
for x in chunk[0].attributes.split(";")}
name = attr_dict[options.naming_attribute]
else:
name = str(chunk[0].attributes)
lcontig = contigs[contig]
positive = Genomics.IsPositiveStrand(strand)
intervals = [(x.start, x.end) for x in chunk]
intervals.sort()
if masks:
if contig in masks:
masked_regions = []
for start, end in intervals:
masked_regions += [(x.start, x.end)
for x in masks[contig].find(start, end)]
masked_regions = Intervals.combine(masked_regions)
if len(masked_regions):
nmasked += 1
if options.remove_masked_regions:
intervals = Intervals.truncate(intervals, masked_regions)
else:
raise "unimplemented"
if len(intervals) == 0:
nskipped_masked += 1
if options.loglevel >= 1:
options.stdlog.write("# skipped because fully masked: "
"%s: regions=%s masks=%s\n" %
(name,
str([(x.start,
x.end) for x in chunk]),
masked_regions))
continue
out = intervals
if options.extend_at and not options.extend_with:
if options.extend_at == "5only":
intervals = [(max(0, intervals[0][0] - options.extend_by),
intervals[0][0])]
elif options.extend_at == "3only":
intervals = [(intervals[-1][1],
min(lcontig,
intervals[-1][1] + options.extend_by))]
else:
if options.extend_at in ("5", "both"):
intervals[0] = (max(0,
intervals[0][0] - options.extend_by),
intervals[0][1])
if options.extend_at in ("3", "both"):
intervals[-1] = (intervals[-1][0],
min(lcontig,
intervals[-1][1] + options.extend_by))
if not positive:
intervals = [(lcontig - x[1], lcontig - x[0])
for x in intervals[::-1]]
out.reverse()
s = [fasta.getSequence(contig, strand, start, end)
for start, end in intervals]
# IMS: allow for masking of sequences
s = Masker.maskSequences(s, options.masker)
l = sum([len(x) for x in s])
if (l < options.min_length or
(options.max_length and l > options.max_length)):
nskipped_length += 1
if options.loglevel >= 1:
options.stdlog.write("# skipped because length out of bounds "
"%s: regions=%s len=%i\n" %
(name, str(intervals), l))
continue
if options.extend_at and options.extend_with:
extension = "".join((options.extend_with,) * options.extend_by)
if options.extend_at in ("5", "both"):
s[1] = extension + s[1]
if options.extend_at in ("3", "both"):
s[-1] = s[-1] + extension
if options.fold_at:
n = options.fold_at
s = "".join(s)
seq = "\n".join([s[i:i+n] for i in range(0, len(s), n)])
else:
seq = "\n".join(s)
options.stdout.write(">%s %s:%s:%s\n%s\n" % (name,
contig,
strand,
";".join(
["%i-%i" %
x for x in out]),
seq))
noutput += 1
E.info("ninput=%i, noutput=%i, nmasked=%i, nskipped_noexons=%i, "
"nskipped_masked=%i, nskipped_length=%i" %
(ninput, noutput, nmasked, nskipped_noexons,
nskipped_masked, nskipped_length))
E.Stop()
def main(argv=None):
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version="%prog version: $Id: gff2fasta.py 2861 2010-02-23 17:36:32Z andreas $")
parser.add_option("-g", "--genome-file", dest="genome_file", type="string",
help="filename with genome.")
parser.add_option("-m", "--masker", dest="masker", type="choice",
choices=("dust", "dustmasker", "softmask", "none"),
help="apply masker [%default].")
parser.add_option("-o", "--mode", dest="mode", type="choice",
choices=("intervals", "leftright"),
help="what to output [%default]")
parser.add_option("--min-length", dest="min_length", type="int",
help="require a minimum sequence length [%default]")
parser.add_option("--max-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 no, 3', 5' or both 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 [default=%default]")
parser.set_defaults(
genome_file=None,
masker=None,
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.mode == "intervals":
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.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("-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 == None: argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: gff2fasta.py 2861 2010-02-23 17:36:32Z andreas $")
parser.add_option("-g",
"--genome-file",
dest="genome_file",
type="string",
help="filename with genome.")
parser.add_option("-m",
"--masker",
dest="masker",
type="choice",
choices=("dust", "dustmasker", "softmask", "none"),
help="apply masker [%default].")
parser.add_option("-o",
"--mode",
dest="mode",
type="choice",
choices=("intervals", "leftright"),
help="what to output [%default]")
parser.add_option("--min-length",
dest="min_length",
type="int",
help="require a minimum sequence length [%default]")
parser.add_option("--max-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 no, 3', 5' or both 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 [default=%default]"
)
parser.set_defaults(
genome_file=None,
masker=None,
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.mode == "intervals":
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.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):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: gff2fasta.py 2861 2010-02-23 17:36:32Z andreas $",
usage=globals()["__doc__"])
parser.add_option("--is-gtf",
dest="is_gtf",
action="store_true",
help="input is gtf instead of gff.")
parser.add_option("-g",
"--genome-file",
dest="genome_file",
type="string",
help="filename with genome [default=%default].")
parser.add_option(
"-m",
"--merge",
dest="merge",
action="store_true",
help="merge adjacent intervals with the same attributes. "
"[default=%default]")
parser.add_option(
"-e",
"--feature",
dest="feature",
type="string",
help="filter by a feature, for example 'exon', 'CDS'. If "
"set to the empty string, all entries are output [%default].")
parser.add_option(
"-f",
"--filename-masks",
dest="filename_masks",
type="string",
metavar="gff",
help="mask sequences with regions given in gff file [%default].")
parser.add_option("--remove-masked-regions",
dest="remove_masked_regions",
action="store_true",
help="remove regions instead of masking [%default].")
parser.add_option(
"--min-length",
dest="min_length",
type="int",
help="set minimum length for sequences output [%default]")
parser.add_option(
"--max-length",
dest="max_length",
type="int",
help="set maximum length for sequences output [%default]")
parser.add_option("--extend-at",
dest="extend_at",
type="choice",
choices=("none", "3", "5", "both", "3only", "5only"),
help="extend at no end, 3', 5' or both 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("--masker",
dest="masker",
type="choice",
choices=("dust", "dustmasker", "softmask", "none"),
help="apply masker [%default].")
parser.set_defaults(is_gtf=False,
genome_file=None,
merge=False,
feature=None,
filename_masks=None,
remove_masked_regions=False,
min_length=0,
max_length=0,
extend_at=None,
extend_by=100,
masker=None)
(options, args) = E.Start(parser)
if options.genome_file:
fasta = IndexedFasta.IndexedFasta(options.genome_file)
contigs = fasta.getContigSizes()
if options.is_gtf:
iterator = GTF.transcript_iterator(GTF.iterator(sys.stdin))
else:
gffs = GTF.iterator(sys.stdin)
if options.merge:
iterator = GTF.joined_iterator(gffs)
else:
iterator = GTF.chunk_iterator(gffs)
masks = None
if options.filename_masks:
masks = {}
with open(options.filename_masks, "r") as infile:
e = GTF.readAsIntervals(GFF.iterator(infile))
# convert intervals to intersectors
for contig in e.keys():
intersector = bx.intervals.intersection.Intersecter()
for start, end in e[contig]:
intersector.add_interval(bx.intervals.Interval(start, end))
masks[contig] = intersector
ninput, noutput, nmasked, nskipped_masked = 0, 0, 0, 0
nskipped_length = 0
nskipped_noexons = 0
feature = options.feature
# for item in iterator:
# print len(item) # 3, 2
# for i in item:
# print len(i) # 9, 9, 9, 9, 9
# print i.contig
# print i.strand
# print i.transcript_id
# iterator is a list containing groups (lists) of features.
# Each group of features have in common the same transcript ID, in case of GTF files.
for ichunk in iterator:
ninput += 1
if feature:
chunk = filter(lambda x: x.feature == feature, ichunk)
else:
chunk = ichunk
if len(chunk) == 0:
nskipped_noexons += 1
E.info("no features in entry from %s:%i..%i - %s" %
(ichunk[0].contig, ichunk[0].start, ichunk[0].end,
str(ichunk[0])))
continue
contig, strand = chunk[0].contig, chunk[0].strand
if options.is_gtf:
name = chunk[0].transcript_id
else:
name = str(chunk[0].attributes)
lcontig = contigs[contig]
positive = Genomics.IsPositiveStrand(strand)
intervals = [(x.start, x.end) for x in chunk]
intervals.sort()
if masks:
if contig in masks:
masked_regions = []
for start, end in intervals:
masked_regions += [(x.start, x.end)
for x in masks[contig].find(start, end)]
masked_regions = Intervals.combine(masked_regions)
if len(masked_regions): nmasked += 1
if options.remove_masked_regions:
intervals = Intervals.truncate(intervals, masked_regions)
else:
raise "unimplemented"
if len(intervals) == 0:
nskipped_masked += 1
if options.loglevel >= 1:
options.stdlog.write( "# skipped because fully masked: %s: regions=%s masks=%s\n" %\
(name, str([ (x.start, x.end) for x in chunk ]), masked_regions) )
continue
out = intervals
if options.extend_at:
if options.extend_at == "5only":
intervals = [(max(0, intervals[0][0] - options.extend_by),
intervals[0][0])]
elif options.extend_at == "3only":
intervals = [(intervals[-1][1],
min(lcontig,
intervals[-1][1] + options.extend_by))]
else:
if options.extend_at in ("5", "both"):
intervals[0] = (max(0,
intervals[0][0] - options.extend_by),
intervals[0][1])
if options.extend_at in ("3", "both"):
intervals[-1] = (intervals[-1][0],
min(lcontig,
intervals[-1][1] + options.extend_by))
if not positive:
intervals = [(lcontig - x[1], lcontig - x[0])
for x in intervals[::-1]]
out.reverse()
s = [
fasta.getSequence(contig, strand, start, end)
for start, end in intervals
]
#IMS: allow for masking of sequences
s = Masker.maskSequences(s, options.masker)
l = sum([len(x) for x in s])
if l < options.min_length or (options.max_length
and l > options.max_length):
nskipped_length += 1
if options.loglevel >= 1:
options.stdlog.write( "# skipped because length out of bounds %s: regions=%s len=%i\n" %\
(name, str(intervals), l) )
continue
options.stdout.write(
">%s %s:%s:%s\n%s\n" %
(name, contig, strand, ";".join(["%i-%i" % x
for x in out]), "\n".join(s)))
noutput += 1
E.info( "ninput=%i, noutput=%i, nmasked=%i, nskipped_noexons=%i, nskipped_masked=%i, nskipped_length=%i" %\
(ninput, noutput, nmasked, nskipped_noexons, nskipped_masked, nskipped_length ) )
E.Stop()
