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The actual contents of the file can be viewed below.

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#! /usr/bin/python

"""
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())