/usr/bin/gffToBed is in pbgenomicconsensus 2.0.0+20151210-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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"""
Convert .gff to .bed format.
"""
import sys
import os
import time
import json
import logging
import argparse
import traceback
from pbcommand.models import FileTypes, get_pbparser
from pbcommand.cli import pbparser_runner
from pbcommand.utils import setup_log
from pbcore.io import GffReader, WriterBase
__version__ = "3.0"
class Constants(object):
TASK_ID = "genomic_consensus.tasks.gff2bed"
PURPOSE_ID = "genomic_consensus.task_options.gff2bed_purpose"
TRACK_NAME_ID = "genomic_consensus.task_options.track_name"
DESCRIPTION_ID = 'genomic_consensus.task_options.track_description'
USE_SCORE_ID = "genomic_consensus.task_options.use_score"
DRIVER_EXE = "gffToBed --resolved-tool-contract "
#
# (Ported from pbpy)
#
class BedRecord:
"""Models a record in a BED file format"""
def __init__(self):
self.chrom=''
self.chromStart = 0
self.chromEnd = 0
self.name = ''
self.score = -1.00
self.strand = '+'
def __str__(self):
return '%s\t%d\t%d\t%s\t%.3f\t%s' % \
(self.chrom, self.chromStart, self.chromEnd, self.name, \
self.score, self.strand)
class CoverageBedRecord(BedRecord):
@staticmethod
def fromAlignmentSummaryGffRecord(gff):
bed = CoverageBedRecord()
bed.chrom = gff.seqid
bed.chromStart = gff.start - 1
bed.chromEnd = gff.end
bed.name = 'meanCov'
bed.score = float(gff.cov2.split(',')[0])
bed.strand = gff.strand
return bed
class VariantsBedRecord(BedRecord):
@staticmethod
def fromVariantGffRecord(gff):
bed = VariantsBedRecord()
bed.chrom = gff.seqid
bed.chromStart = gff.start - 1
bed.score = float(gff.confidence)
bed.strand = gff.strand
feature = gff.type
#GFF3 coordinates are 1-based and inclusive
#BED coordinates are 0-based and exclusive
if feature == 'insertion':
bed.chromEnd = bed.chromStart + 1
bed.name = '%d_%dins%s' % (bed.chromStart + 1,
bed.chromEnd + 1,
gff.variantSeq)
elif feature == 'deletion':
featureLen = len(gff.reference)
bed.chromEnd = bed.chromStart + featureLen
if featureLen == 1:
bed.name = "%ddel" % (bed.chromStart + 1)
else:
bed.name = '%d_%ddel' % (bed.chromStart + 1, bed.chromEnd)
elif feature == 'substitution':
bed.chromEnd = bed.chromStart + 1
bed.name = '%d%s>%s' % (bed.chromStart + 1,
gff.reference,
gff.variantSeq)
else:
print >> sys.stderr, 'Unsupported feature %s found in GFF3 file.' % feature
return bed
class BedWriter(WriterBase):
"""Outputs BED annotation track file"""
def __init__(self, outfile):
self._outfile = outfile
def close(self):
self._outfile.close()
def flush(self):
self._outfile.flush()
def writeHeader(self, name, description, useScore):
print >> self._outfile, 'track name=%s description="%s" useScore=%d' \
% (name, description, useScore)
def writeRecord(self, record):
print >> self._outfile, str(record)
class GffToBed:
"""
Utility for converting GFF3 to BED format. Currently supports
regional coverage or variant .bed output.
"""
def __init__(self, args):
self.purpose = args.purpose
self.gffFile = args.gff
self.args = args
if self.purpose not in [ "variants", "coverage" ]:
raise ValueError(
"Purpose %s not supported. Must be one of: [variants|coverage]" % (self.purpose))
def run(self, out=sys.stdout):
with GffReader(self.gffFile) as reader, \
BedWriter(out) as writer:
writer.writeHeader(self.args.name,
self.args.description,
self.args.useScore)
for gff in reader:
if self.purpose == 'coverage':
bedRecord = CoverageBedRecord.fromAlignmentSummaryGffRecord(gff)
else:
bedRecord = VariantsBedRecord.fromVariantGffRecord(gff)
writer.writeRecord(bedRecord)
return 0
def args_runner(args, out=sys.stdout):
return GffToBed(args).run(out=out)
def resolved_tool_contract_runner(resolved_tool_contract):
rtc = resolved_tool_contract
assert rtc.task.options[Constants.PURPOSE_ID] in ["coverage", "variants"]
args = [
rtc.task.options[Constants.PURPOSE_ID],
rtc.task.input_files[0],
"--useScore", str(rtc.task.options[Constants.USE_SCORE_ID]),
# "--name", str(rtc.task.options[Constants.TRACK_NAME_ID]),
# "--description", str(rtc.task.options[Constants.DESCRIPTION_ID]),
]
# XXX HACK
args_ = get_contract_parser().arg_parser.parser.parse_args(args)
with open(rtc.task.output_files[0], "w") as f:
return args_runner(args_, out=f)
def get_contract_parser():
p = get_pbparser(
tool_id=Constants.TASK_ID,
version=__version__,
name="gffToBed",
description=__doc__,
driver_exe=Constants.DRIVER_EXE)
ap = p.arg_parser.parser
tcp = p.tool_contract_parser
ap.add_argument("purpose", choices=["variants","coverage"],
help="Run purpose")
p.add_input_file_type(FileTypes.GFF, "gff",
"GFF file", "GFF file")
tcp.add_output_file_type(FileTypes.BED, "bed",
"BED file", "BED file", "output.bed")
tcp.add_str(Constants.PURPOSE_ID, "purpose",
default="",
name="Purpose",
description="Run mode ('variants' or 'coverage')")
p.add_str(Constants.TRACK_NAME_ID, "name",
default="variants",
name="Track name",
description="track name to display in header")
p.add_str(Constants.DESCRIPTION_ID, 'description',
default="PacBio: snps, insertions, and deletions derived from consensus calls against reference",
name="Track description",
description="track description to display in header")
p.add_int(Constants.USE_SCORE_ID, "useScore",
default=0,
name="Use score",
description="whether or not to use score for feature display")
return p
def main(argv=sys.argv):
logging.basicConfig(level=logging.WARN)
log = logging.getLogger()
mp = get_contract_parser()
def dummy_log(*args, **kwargs):
pass
return pbparser_runner(
argv=argv[1:],
parser=mp,
args_runner_func=args_runner,
contract_runner_func=resolved_tool_contract_runner,
alog=log,
setup_log_func=dummy_log)
if __name__ == '__main__':
sys.exit(main())
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