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.ArgumentParser(description=__doc__)
parser.add_argument("--version", action='version', version="1.0")
parser.add_argument("-g",
"--genome-file",
dest="genome_file",
type=str,
help="filename with genome (indexed).")
parser.add_argument("-w",
"--windows-bed-file",
dest="filename_windows",
type=str,
help="gff file with windows to use.")
parser.add_argument("-d",
"--filename-data",
dest="filename_data",
type=str,
help="gff file with data to use.")
parser.add_argument("--is-gtf",
dest="is_gtf",
action="store_true",
help="filename-data is gtf file")
parser.add_argument("-f",
"--features",
dest="features",
type=str,
action="append",
choices=("GC", ),
help="features to compute.")
parser.add_argument("-c",
"--decorator",
dest="decorator",
type=str,
choices=("counts", "gc", "gc3", "mean-length",
"median-length", "percent-coverage",
"median-score", "mean-score", "stddev-score",
"min-score", "max-score"),
help="decorators to use.")
parser.add_argument("-e",
"--skip-empty",
dest="skip_empty",
action="store_true",
help="skip empty windows.")
parser.add_argument(
"-t",
"--transform=",
dest="transform",
type=str,
choices=("none", "overlap", "complement", "third_codon"),
help="transform to use when mapping overlapping regions onto window.")
parser.set_defaults(
genome_file=None,
filename_windows=None,
filename_data=None,
features=[],
skip_empty=False,
decorator="counts",
transform="none",
is_gtf=False,
)
(args) = E.start(parser)
# test_transform_third_codon()
if not args.filename_windows:
raise ValueError("please supply a gff file with window information.")
if args.loglevel >= 1:
args.stdlog.write("# reading windows...")
args.stdlog.flush()
windows = GTF.readAsIntervals(
GTF.iterator(iotools.open_file(args.filename_windows, "r")))
if args.loglevel >= 1:
args.stdlog.write("done\n")
args.stdlog.flush()
if args.filename_data:
if args.loglevel >= 1:
args.stdlog.write("# reading data...")
args.stdlog.flush()
if args.is_gtf:
gff_data = GTF.readFromFile(
iotools.open_file(args.filename_data, "r"))
else:
gff_data = GTF.readFromFile(
IOTOols.open_file(args.filename_data, "r"))
if args.loglevel >= 1:
args.stdlog.write("done\n")
args.stdlog.flush()
data_ranges = GTF.SortPerContig(gff_data)
else:
# use windows to compute properties
# by supplying no data and asking for the complement = original window
gff_data = None
data_ranges = None
args.transform = "complement"
map_contig2size = {}
if args.genome_file:
fasta = IndexedFasta.IndexedFasta(args.genome_file)
map_contig2size = fasta.getContigSizes()
else:
for contig, values in list(windows.items()):
map_contig2size[contig] = max(lambda x: x[1], values)
fasta = None
contigs = list(map_contig2size.keys())
contigs.sort()
# proceed contig wise
noutput_contigs, ncontigs_skipped_windows, ncontigs_skipped_data = 0, 0, 0
args.stdout.write("\t".join(
map(str, ("contig", "start", "end", "ngenes", "ntranscripts", "n1",
"l1", "n2", "l2", "score", "extra_info"))) + "\n")
for contig in contigs:
skip = False
if contig not in windows:
ncontigs_skipped_windows += 1
skip = True
if data_ranges and contig not in data_ranges:
ncontigs_skipped_data += 1
skip = True
if skip:
continue
noutput_contigs += 1
if data_ranges:
annotateWindows(
contig, windows[contig],
gff_data[data_ranges[contig][0]:data_ranges[contig][1]], fasta,
args)
else:
annotateWindows(contig, windows[contig], [], fasta, args)
E.info(
"ninput_windows=%i, noutput_contigs=%i, ninput_contigs=%i, nskipped_windows=%i, nskipped_data=%i"
% (len(windows), noutput_contigs, len(contigs),
ncontigs_skipped_windows, ncontigs_skipped_data))
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("--header-attributes",
dest="header_attr",
action="store_true",
help="add GFF entry attributes to the FASTA record"
" header section")
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,
header_attr=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.open_file(options.filename_masks, "r") as infile:
e = GTF.readAsIntervals(GTF.iterator(infile))
# convert intervals to intersectors
for contig in list(e.keys()):
intersector = quicksect.IntervalTree()
for start, end in e[contig]:
intersector.add(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(
quicksect.Interval(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)
if options.header_attr:
attributes = " ".join(
[":".join([ax, ay]) for ax, ay in chunk[0].asDict().items()])
options.stdout.write(
">%s %s:%s:%s feature:%s %s\n%s\n" %
(name, contig, strand, ";".join(
["%i-%i" % x
for x in out]), chunk[0].feature, attributes, seq))
else:
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 cropGFF(gffs, filename_gff):
"""crop intervals in gff file."""
# read regions to crop with and convert intervals to intersectors
E.info("reading gff for cropping: started.")
other_gffs = GTF.iterator(iotools.open_file(filename_gff, "r"))
cropper = GTF.readAsIntervals(other_gffs)
ntotal = 0
for contig in list(cropper.keys()):
intersector = quicksect.IntervalTree()
for start, end in cropper[contig]:
intersector.add(start, end)
ntotal += 1
cropper[contig] = intersector
E.info("reading gff for cropping: finished.")
E.info("reading gff for cropping: %i contigs with %i intervals." %
(len(cropper), ntotal))
ninput, noutput, ncropped, ndeleted = 0, 0, 0, 0
# do the actual cropping
for gff in gffs:
ninput += 1
if gff.contig in cropper:
start, end = gff.start, gff.end
overlaps = cropper[gff.contig].find(quicksect.Interval(start, end))
if overlaps:
l = end - start
a = numpy.ones(l)
for i in overlaps:
s = max(0, i.start - start)
e = min(l, i.end - start)
a[s:e] = 0
segments = Intervals.fromArray(a)
if len(segments) == 0:
ndeleted += 1
else:
ncropped += 1
for s, e in segments:
gff.start, gff.end = s + start, e + start
noutput += 1
yield (gff)
continue
noutput += 1
yield (gff)
E.info("ninput=%i, noutput=%i, ncropped=%i, ndeleted=%i" %
(ninput, noutput, ncropped, ndeleted))
