def testIteratorUncompressed(self):
'''test iteration from uncompressed file.'''
tmpfilename = 'tmp_testIteratorUncompressed'
infile = gzip.open(self.filename, "rb")
outfile = open(tmpfilename, "wb")
outfile.write(infile.read())
outfile.close()
infile.close()
with open(tmpfilename) as infile:
for x, r in enumerate(pysam.tabix_iterator(infile,
pysam.asTuple())):
self.assertEqual(self.compare[x], list(r))
self.assertEqual(len(self.compare[x]), len(r))
# test indexing
for c in range(0, len(r)):
self.assertEqual(self.compare[x][c], r[c])
# test slicing access
for c in range(0, len(r) - 1):
for cc in range(c + 1, len(r)):
self.assertEqual(self.compare[x][c:cc], r[c:cc])
os.unlink(tmpfilename)
def testIteratorUncompressed(self):
'''test iteration from uncompressed file.'''
tmpfilename = 'tmp_testIteratorUncompressed'
infile = gzip.open(self.filename, "rb")
outfile = open(tmpfilename, "wb")
outfile.write(infile.read())
outfile.close()
infile.close()
with open(tmpfilename) as infile:
for x, r in enumerate(pysam.tabix_iterator(
infile, pysam.asTuple())):
self.assertEqual(self.compare[x], list(r))
self.assertEqual(len(self.compare[x]), len(r))
# test indexing
for c in range(0, len(r)):
self.assertEqual(self.compare[x][c], r[c])
# test slicing access
for c in range(0, len(r) - 1):
for cc in range(c + 1, len(r)):
self.assertEqual(self.compare[x][c:cc],
r[c:cc])
os.unlink(tmpfilename)
def filter_bam(args, bcd):
with open(args.output, 'w') as o:
with gzip.open(args.fragments) as f:
tbx = pysam.tabix_iterator(f, pysam.asBed())
for line in tbx:
if line.name in bcd:
o.write("{}\n".format(str(line)))
return 0
def filter_bam(args,bcd):
reads = {}
replicate = {}
with gzip.open(args.fragments) as f:
tbx = pysam.tabix_iterator(f,pysam.asBed())
for line in tbx:
if line.name in bcd:
try:
reads[bcd[line.name] + "_rep" + line.name.split("_")[-2]].append(str(line))
except KeyError:
reads[bcd[line.name] + "_rep" + line.name.split("_")[-2]] = [str(line)]
return(reads)
def testIteratorCompressed(self):
"""test iteration from compressed file."""
with gzip.open(self.filename) as infile:
for x, r in enumerate(pysam.tabix_iterator(infile, pysam.asTuple())):
self.assertEqual(self.compare[x], list(r))
self.assertEqual(len(self.compare[x]), len(r))
# test indexing
for c in range(0, len(r)):
self.assertEqual(self.compare[x][c], r[c])
# test slicing access
for c in range(0, len(r) - 1):
for cc in range(c + 1, len(r)):
self.assertEqual(self.compare[x][c:cc], r[c:cc])
def testIteratorCompressed(self):
'''test iteration from compressed file.'''
with gzip.open(self.filename) as infile:
for x, r in enumerate(pysam.tabix_iterator(infile,
pysam.asTuple())):
self.assertEqual(self.compare[x], list(r))
self.assertEqual(len(self.compare[x]), len(r))
# test indexing
for c in range(0, len(r)):
self.assertEqual(self.compare[x][c], r[c])
# test slicing access
for c in range(0, len(r) - 1):
for cc in range(c + 1, len(r)):
self.assertEqual(self.compare[x][c:cc], r[c:cc])
def GetSumOfDifferencesFromTheReference(vcfpath):
from subprocess import check_call
from utilBMF.HTSUtils import TrimExt
import pysam
import numpy as np
from sys import stderr
from itertools import chain
cfi = chain.from_iterable
bgvcfpath = TrimExt(vcfpath) + ".gz"
check_call("bgzip -c %s > %s" % (vcfpath, bgvcfpath), shell=True)
stderr.write("bgvcf now at %s" % bgvcfpath)
tabixstr = "tabix " + bgvcfpath
stderr.write("Now calling tabixstr: '%s'" % tabixstr)
check_call("tabix %s" % bgvcfpath, shell=True)
infh = open(bgvcfpath, "rb")
tabixhandle = pysam.tabix_iterator(infh, pysam.asVCF())
return np.sum(np.array(list(cfi([dict(tup.split("=") for
tup in i.info.split(";"))[
'I16'].split(",")[2:4] for i in tabixhandle if
"INDEL" not in i.info])), dtype=np.int64))
def main():
logging.basicConfig(level=logging.DEBUG)
parser = argparse.ArgumentParser()
parser.add_argument('--frac', type=float, default=0.0)
parser.add_argument('gtf_file')
args = parser.parse_args()
all_t_ids = set()
t_ids = set()
for f in pysam.tabix_iterator(open(args.gtf_file), pysam.asGTF()):
if f.feature == 'transcript':
t_id = f.transcript_id
frac = float(f.frac)
keep = (frac >= args.frac)
all_t_ids.add(t_id)
if keep:
t_ids.add(t_id)
print str(f)
elif f.feature == 'exon':
t_id = f.transcript_id
assert t_id in all_t_ids
if t_id in t_ids:
print str(f)
def main():
logging.basicConfig(level=logging.DEBUG)
parser = argparse.ArgumentParser()
parser.add_argument('--frac', type=float, default=0.0)
parser.add_argument('gtf_file')
args = parser.parse_args()
all_t_ids = set()
t_ids = set()
for f in pysam.tabix_iterator(open(args.gtf_file), pysam.asGTF()):
if f.feature == 'transcript':
t_id = f.transcript_id
frac = float(f.frac)
keep = (frac >= args.frac)
all_t_ids.add(t_id)
if keep:
t_ids.add(t_id)
print str(f)
elif f.feature == 'exon':
t_id = f.transcript_id
assert t_id in all_t_ids
if t_id in t_ids:
print str(f)
def iterator(infile):
"""return a simple iterator over all entries in a file."""
return pysam.tabix_iterator(infile, pysam.asGTF())
def main(argv=sys.argv):
# setup command line parser
parser = E.ArgumentParser(description=__doc__)
parser.add_argument("-s",
"--session",
dest="session",
type=str,
help="load session before creating plots ")
parser.add_argument("-d",
"--snapshot-dir",
dest="snapshotdir",
type=str,
help="directory to save snapshots in ")
parser.add_argument("-f",
"--format",
dest="format",
type=str,
choices=("png", "eps", "svg"),
help="output file format ")
parser.add_argument("-o",
"--host",
dest="host",
type=str,
help="host that IGV is running on ")
parser.add_argument("-p",
"--port",
dest="port",
type=int,
help="port that IGV listens at ")
parser.add_argument("-e",
"--extend",
dest="extend",
type=int,
help="extend each interval by a number of bases ")
parser.add_argument("-x",
"--expand",
dest="expand",
type=float,
help="expand each region by a certain factor ")
parser.add_argument("--session-only",
dest="session_only",
action="store_true",
help="plot session after opening, "
"ignore intervals ")
parser.add_argument("-n",
"--name",
dest="name",
type=str,
choices=("bed-name", "increment"),
help="name to use for snapshot ")
parser.set_defaults(
command="igv.sh",
host='127.0.0.1',
port=61111,
snapshotdir=os.getcwd(),
extend=0,
format="png",
expand=1.0,
session=None,
session_only=False,
keep_open=False,
name="bed-name",
)
# add common options (-h/--help, ...) and parse command line
(args) = E.start(parser, argv=argv, add_output_options=True)
igv_process = None
if args.new_instance:
E.info("starting new IGV process")
igv_process = IGV.startIGV(command=args.command, port=args.port)
E.info("new IGV process started")
E.info("connection to process on %s:%s" % (args.host, args.port))
E.info("saving images in %s" % args.snapshotdir)
igv = IGV(host=args.host,
port=args.port,
snapshot_dir=os.path.abspath(args.snapshotdir))
if args.session:
E.info('loading session from %s' % args.session)
igv.load(args.session)
E.info('loaded session')
if args.session_only:
E.info('plotting session only ignoring any intervals')
fn = "%s.%s" % (os.path.basename(args.session), args.format)
E.info("writing snapshot to '%s'" % os.path.join(args.snapshotdir, fn))
igv.save(fn)
else:
c = E.Counter()
for bed in pysam.tabix_iterator(args.stdin, parser=pysam.asBed()):
c.input += 1
# IGV can not deal with white-space in filenames
if args.name == "bed-name":
name = re.sub("\s", "_", bed.name)
elif args.name == "increment":
name = str(c.input)
E.info("going to %s:%i-%i for %s" %
(bed.contig, bed.start, bed.end, name))
start, end = bed.start, bed.end
extend = args.extend
if args.expand:
d = end - start
extend = max(extend, (args.expand * d - d) // 2)
start -= extend
end += extend
igv.go("%s:%i-%i" % (bed.contig, start, end))
fn = E.get_output_file("%s.%s" % (name, args.format))
E.info("writing snapshot to '%s'" % fn)
igv.save(fn)
c.snapshots += 1
E.info(c)
if igv_process is not None and not args.keep_open:
E.info('shutting down IGV')
igv_process.send_signal(signal.SIGKILL)
E.stop()
def main(argv=sys.argv):
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-b",
"--reference-bed-file",
dest="reference_bed_file",
type="string",
help="reference bed file "
"[%default]")
parser.add_option("-m",
"--method",
dest="method",
type="choice",
choices=("lvc-comparison", ),
help="methods to apply [%default]")
parser.set_defaults(method="lvc-comparison",
reference_fasta_file=None,
input_bed_file=None,
size_bins=(1000, 10000, 100000),
output_sets=True,
region_string=None)
# add common options (-h/--help, ...) and parse command line
(options, args) = E.start(parser, argv=argv, add_output_options=True)
reference_set = collections.defaultdict(quicksect.IntervalTree)
E.info("reading reference bed file from {}".format(
options.reference_bed_file))
with IOTools.open_file(options.reference_bed_file) as inf:
for record in pysam.tabix_iterator(inf, pysam.asBed()):
mm = reference_set[record.contig]
mm.add(record.start, record.end)
E.info("read reference intervals on {} contigs: {}".format(
len(list(reference_set.keys())), ",".join(list(reference_set.keys()))))
if options.output_sets:
output_tp = E.open_output_file("tp")
output_fp = E.open_output_file("fp")
output_fn = E.open_output_file("fn")
else:
output_tp = None
output_fp = None
output_fn = None
if options.method == "lvc-comparison":
c = E.Counter()
found = set()
counts = {}
names = set()
nsize_bins = len(options.size_bins)
for bin in range(len(options.size_bins) + 1):
counts[bin] = dict([(x, collections.defaultdict(int))
for x in ("tp", "fn", "fp", "test", "truth")])
for record in pysam.tabix_iterator(options.stdin, pysam.asBed()):
if record.contig not in reference_set:
c.ignored_no_contig += 1
continue
c.test += 1
matches = reference_set[record.contig].search(
record.start, record.end)
size = record.end - record.start
bin = get_size_bin(size, options.size_bins)
if len(matches) == 0:
c.fp += 1
status = "fp"
if output_fp:
output_fp.write(str(record) + "\n")
elif len(matches) >= 1:
c.tp += 1
status = "tp"
if output_tp:
output_tp.write(str(record) + "\n")
# todo: overlap criteria
# record found
for match in matches:
found.add((record.contig, match.start, match.end))
name = record.name.split(",")[0]
names.add(name)
counts[bin]["test"][name] += 1
counts[bin][status][name] += 1
outf = options.stdout
with IOTools.open_file(options.reference_bed_file) as inf:
for record in pysam.tabix_iterator(inf, pysam.asBed()):
c.truth += 1
bin = get_size_bin(record.end - record.start,
options.size_bins)
counts[bin]["truth"]["all"] += 1
key = (record.contig, record.start, record.end)
if key not in found:
c.fn += 1
counts[bin]["fn"]["all"] += 1
outf.write("\t".join(("category", "size", "test", "tp", "fp", "truth",
"fn")) + "\n")
for name in sorted(names):
for bin in range(len(options.size_bins) + 1):
if bin == len(options.size_bins):
size_bin = ">={}".format(options.size_bins[-1])
else:
size_bin = "<{}".format(options.size_bins[bin])
outf.write("\t".join(
map(str, (
name,
size_bin,
counts[bin]["test"][name],
counts[bin]["tp"][name],
counts[bin]["fp"][name],
counts[bin]["truth"]["all"],
counts[bin]["fn"]["all"],
))) + "\n")
E.info(str(c))
E.stop()
def _aggregate_gtf(gtf_file, sample_id, gtf_expr_attr, output_fh, stats_fh,
is_ref=False):
def _init_t_dict():
return {'_id': None, 'num_exons': 0, 'length': 0}
t_dict = collections.defaultdict(_init_t_dict)
cur_t_id = 1
exprs = []
for f in pysam.tabix_iterator(open(gtf_file), pysam.asGTF()):
if f.feature == 'transcript':
t_id = f.transcript_id
if t_id in t_dict:
m = 'GTF "%s" transcript_id "%s" not unique' % (gtf_file, t_id)
raise GTFError(m)
t_item = t_dict[t_id]
# rename transcript id
new_t_id = "%s.T%d" % (sample_id, cur_t_id)
cur_t_id += 1
t_item['_id'] = new_t_id
if is_ref:
expr = 0.0
else:
expr = float(f[gtf_expr_attr])
exprs.append(expr)
# prepare attributes
attrs = {GTF.Attr.TRANSCRIPT_ID: new_t_id,
GTF.Attr.SAMPLE_ID: sample_id,
GTF.Attr.REF: str(int(is_ref)),
GTF.Attr.EXPR: str(expr)}
# save attributes
f.fromDict(attrs)
print >>output_fh, str(f)
elif f.feature == 'exon':
t_id = f.transcript_id
t_item = t_dict[t_id]
# update statistics
t_item['num_exons'] += 1
t_item['length'] += (f.end - f.start)
# replace transcript id
f.fromDict({GTF.Attr.TRANSCRIPT_ID: t_item['_id']})
print >>output_fh, str(f)
# process statistics
num_exons = []
lengths = []
for t_item in t_dict.itervalues():
lengths.append(t_item['length'])
num_exons.append(t_item['num_exons'])
# compute and write stats
quantiles = range(0, 101)
expr_qs = (scoreatpercentile(exprs, q) for q in quantiles)
expr_qs = ','.join(map(str, expr_qs))
length_qs = (int(round(scoreatpercentile(lengths, q)))
for q in quantiles)
length_qs = ','.join(map(str, length_qs))
num_exon_qs = (int(round(scoreatpercentile(num_exons, q)))
for q in quantiles)
num_exon_qs = ','.join(map(str, num_exon_qs))
fields = [sample_id, len(t_dict), expr_qs, length_qs, num_exon_qs]
print >>stats_fh, '\t'.join(map(str, fields))
def iterate_parsed_uncompressed(fn):
with open(fn) as f:
return len(list(pysam.tabix_iterator(f, parser=pysam.asBed())))
def test_iterator_parsed_compressed():
f = gzip.open(fn_compressed)
l = len( list( pysam.tabix_iterator( f, parser = pysam.asBed() )))
def test_iterator_parsed_uncompressed():
f = open("windows_small.bed")
l = len(list(pysam.tabix_iterator(f, parser=pysam.asBed())))
def readFromFile(infile):
"""read records from file and return as list."""
result = []
for gff in pysam.tabix_iterator(infile, pysam.asGTF()):
result.append(gff)
return result
def test_iterator_parsed_compressed():
f = gzip.open(fn_compressed)
l = len(list(pysam.tabix_iterator(f, parser=pysam.asBed())))
def readFromFile( infile ):
"""read gtf from file."""
result = []
for gff in pysam.tabix_iterator( infile, pysam.asGTF() ):
result.append( gff )
return result
def readFromFile(infile):
"""read gtf from file."""
result = []
for gff in pysam.tabix_iterator(infile, pysam.asGTF()):
result.append(gff)
return result
def test_iterator_parsed_uncompressed():
f = open("windows_small.bed")
l = len( list( pysam.tabix_iterator( f, parser = pysam.asBed() )))
def readFromFile(infile):
"""read records from file and return as list."""
result = []
for gff in pysam.tabix_iterator(infile, pysam.asGTF()):
result.append(gff)
return result
def main(argv=None):
'''
main function
'''
if argv is None:
argv = sys.argv
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-g",
"--is-gff3",
dest="gff3_input",
action="store_true",
help="filename in gff3 format"
"[default=%default].")
parser.add_option("-o",
"--output-only-attributes",
dest="only_attributes",
action="store_true",
help="output only attributes as separate columns "
"[default=%default].")
parser.add_option("-f",
"--attributes-as-columns",
dest="output_full",
action="store_true",
help="output attributes as separate columns "
"[default=%default].")
parser.add_option("-i",
"--invert",
dest="invert",
action="store_true",
help="convert tab-separated table back to gtf "
"[default=%default].")
parser.add_option("-m",
"--output-map",
dest="output_map",
type="choice",
choices=("transcript2gene", "peptide2gene",
"peptide2transcript"),
help="output a map mapping transcripts to genes "
"[default=%default].")
parser.set_defaults(only_attributes=False,
output_full=False,
invert=False,
output_map=None,
gff3_input=False)
(options, args) = E.Start(parser, argv=argv)
if options.output_full:
# output full table with column for each attribute
# to specify gff3 format
if options.gff3_input is True:
gff = pysam.tabix_iterator(options.stdin, parser=pysam.asGFF3())
attributes = set()
data = []
for line in gff:
# get keys to write out to header
data.append(line)
attributes = attributes.union(set(line.keys()))
attributes = sorted(list(attributes))
header = [
"contig", "source", "feature", "start", "end", "score",
"strand", "frame"
] + attributes
options.stdout.write("\t".join(header) + "\n")
for gff3 in data:
for a in header:
val = getattr(gff3, a)
options.stdout.write("%s\t" % (val))
options.stdout.write("\n")
else:
attributes = set()
data = []
for gtf in GTF.iterator(options.stdin):
data.append(gtf)
attributes = attributes.union(set(gtf.keys()))
# remove gene_id and transcript_id, as they are used
# explicitely later
attributes.difference_update(["gene_id", "transcript_id"])
attributes = sorted(list(attributes))
if options.only_attributes:
header = ["gene_id", "transcript_id"] + attributes
else:
header = [
"contig",
"source",
"feature",
"start",
"end",
"score",
"strand",
"frame",
"gene_id",
"transcript_id",
] + attributes
options.stdout.write("\t".join(header) + "\n")
if options.only_attributes:
for gtf in data:
options.stdout.write("\t".join(
map(str, (
gtf.gene_id,
gtf.transcript_id,
))))
for a in attributes:
if a in ("gene_id", "transcript_id"):
continue
try:
val = getattr(gtf, a)
except AttributeError:
val = ""
except KeyError:
val = ""
options.stdout.write("\t%s" % val)
options.stdout.write("\n")
else:
for gtf in data:
options.stdout.write("\t".join(
map(str, (
gtf.contig,
gtf.source,
gtf.feature,
gtf.start,
gtf.end,
gtf.score,
gtf.strand,
gtf.frame,
gtf.gene_id,
gtf.transcript_id,
))))
for a in attributes:
try:
val = getattr(gtf, a)
except AttributeError:
val = ""
options.stdout.write("\t%s" % val)
options.stdout.write("\n")
elif options.invert:
gtf = GTF.Entry()
header = None
for line in options.stdin:
if line.startswith("#"):
continue
data = line[:-1].split("\t")
if not header:
header = data
map_header2column = dict([(y, x)
for x, y in enumerate(header)])
continue
# fill gtf entry with data
try:
gtf.contig = data[map_header2column["contig"]]
gtf.source = data[map_header2column["source"]]
gtf.feature = data[map_header2column["feature"]]
# subtract -1 to start for 0-based coordinates
gtf.start = int(data[map_header2column["start"]])
gtf.end = int(data[map_header2column["end"]])
gtf.score = data[map_header2column["score"]]
gtf.strand = data[map_header2column["strand"]]
gtf.frame = data[map_header2column["frame"]]
gtf.gene_id = data[map_header2column["gene_id"]]
gtf.transcript_id = data[map_header2column["transcript_id"]]
gtf.parseInfo(data[map_header2column["attributes"]], line)
except KeyError as msg:
raise KeyError("incomplete entry %s: %s: %s" %
(str(data), str(map_header2column), msg))
# output gtf entry in gtf format
options.stdout.write("%s\n" % str(gtf))
elif options.output_map:
if options.output_map == "transcript2gene":
fr = lambda x: x.transcript_id
to = lambda x: x.gene_id
options.stdout.write("transcript_id\tgene_id\n")
elif options.output_map == "peptide2gene":
fr = lambda x: x.protein_id
to = lambda x: x.gene_id
options.stdout.write("peptide_id\tgene_id\n")
elif options.output_map == "peptide2transcript":
fr = lambda x: x.protein_id
to = lambda x: x.transcript_id
options.stdout.write("peptide_id\ttranscript_id\n")
map_fr2to = {}
for gtf in GTF.iterator(options.stdin):
try:
map_fr2to[fr(gtf)] = to(gtf)
except AttributeError:
pass
for x, y in sorted(map_fr2to.items()):
options.stdout.write("%s\t%s\n" % (x, y))
else:
header = ("contig", "source", "feature", "start", "end", "score",
"strand", "frame", "gene_id", "transcript_id", "attributes")
options.stdout.write("\t".join(header) + "\n")
for gtf in GTF.iterator(options.stdin):
attributes = []
for a in list(gtf.keys()):
if a in ("gene_id", "transcript_id"):
continue
attributes.append('%s %s' % (a, GTF.quote(gtf[a])))
attributes = "; ".join(attributes)
options.stdout.write("\t".join(
map(str, (
gtf.contig,
gtf.source,
gtf.feature,
gtf.start,
gtf.end,
GTF.toDot(gtf.score),
gtf.strand,
gtf.frame,
gtf.gene_id,
gtf.transcript_id,
attributes,
))) + "\n")
E.Stop()
def __init__(self, infile, *args, **kwargs):
self.gff = pysam.tabix_iterator(iotools.open_file(infile),
parser=pysam.asGFF3())
def _aggregate_gtf(gtf_file,
sample_id,
gtf_expr_attr,
output_fh,
stats_fh,
is_ref=False):
def _init_t_dict():
return {'_id': None, 'num_exons': 0, 'length': 0}
t_dict = collections.defaultdict(_init_t_dict)
cur_t_id = 1
exprs = []
for f in pysam.tabix_iterator(open(gtf_file), pysam.asGTF()):
if f.feature == 'transcript':
t_id = f.transcript_id
if t_id in t_dict:
m = 'GTF "%s" transcript_id "%s" not unique' % (gtf_file, t_id)
raise GTFError(m)
t_item = t_dict[t_id]
# rename transcript id
new_t_id = "%s.T%d" % (sample_id, cur_t_id)
cur_t_id += 1
t_item['_id'] = new_t_id
if is_ref:
expr = 0.0
else:
expr = float(f[gtf_expr_attr])
exprs.append(expr)
# prepare attributes
attrs = {
GTF.Attr.TRANSCRIPT_ID: new_t_id,
GTF.Attr.SAMPLE_ID: sample_id,
GTF.Attr.REF: str(int(is_ref)),
GTF.Attr.EXPR: str(expr)
}
# save attributes
f.fromDict(attrs)
print >> output_fh, str(f)
elif f.feature == 'exon':
t_id = f.transcript_id
t_item = t_dict[t_id]
# update statistics
t_item['num_exons'] += 1
t_item['length'] += (f.end - f.start)
# replace transcript id
f.fromDict({GTF.Attr.TRANSCRIPT_ID: t_item['_id']})
print >> output_fh, str(f)
# process statistics
num_exons = []
lengths = []
for t_item in t_dict.itervalues():
lengths.append(t_item['length'])
num_exons.append(t_item['num_exons'])
# compute and write stats
quantiles = range(0, 101)
expr_qs = (scoreatpercentile(exprs, q) for q in quantiles)
expr_qs = ','.join(map(str, expr_qs))
length_qs = (int(round(scoreatpercentile(lengths, q))) for q in quantiles)
length_qs = ','.join(map(str, length_qs))
num_exon_qs = (int(round(scoreatpercentile(num_exons, q)))
for q in quantiles)
num_exon_qs = ','.join(map(str, num_exon_qs))
fields = [sample_id, len(t_dict), expr_qs, length_qs, num_exon_qs]
print >> stats_fh, '\t'.join(map(str, fields))
def get_bed_dict(refdict, bedfh):
beddict = {chrom: np.zeros(len(refdict[chrom]), dtype = np.bool) for chrom in refdict.keys()}
for bedline in pysam.tabix_iterator(bedfh, parser = pysam.asBed()):
beddict[bedline.contig][bedline.start:bedline.end] = True #end is 1 past the actual end, so this slice should work properly
return beddict
def iterate_parsed_uncompressed(fn):
with open(fn) as f:
return len(list(pysam.tabix_iterator(f, parser=pysam.asBed())))
def iterator(infile):
"""return a simple iterator over all entries in a file."""
return pysam.tabix_iterator(infile, pysam.asGTF())
def __init__(self, infile, *args, **kwargs):
self.gff = pysam.tabix_iterator(IOTools.openFile(infile),
parser=pysam.asGFF3())