/usr/bin/summarizeConsensus 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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"""
Augment the alignment_summary.gff file with consensus and variants information.
"""
from collections import namedtuple
import argparse
import logging
import json
import gzip
import sys
import numpy as np
from pbcommand.utils import setup_log
from pbcommand.cli import pacbio_args_or_contract_runner, get_default_argparser
from pbcommand.models import FileTypes, get_pbparser
from pbcommand.common_options import add_resolved_tool_contract_option
from pbcore.io import GffReader, GffWriter, Gff3Record
from GenomicConsensus.utils import error_probability_to_qv
from GenomicConsensus import __VERSION__
#
# Note: GFF-style coordinates
#
Region = namedtuple("Region", ("seqid", "start", "end"))
class Constants(object):
TOOL_ID = "genomic_consensus.tasks.summarize_consensus"
DRIVER_EXE = "summarizeConsensus --resolved-tool-contract "
def get_argument_parser():
parser = get_default_argparser(__VERSION__, __doc__)
parser.add_argument("inputAlignmentSummaryGff",
type=str,
help="Input alignment_summary.gff filename")
# FIXME not optional, should be positional
parser.add_argument("--variantsGff",
type=str,
help="Input variants.gff or variants.gff.gz filename",
required=True)
parser.add_argument("--output",
"-o",
type=str,
help="Output alignment_summary.gff filename")
add_resolved_tool_contract_option(parser)
# FIXME temporary workaround for parser chaos
class EmitToolContractAction(argparse.Action):
def __call__(self, parser, namespace, values, option_string=None):
parser2 = get_contract_parser()
sys.stdout.write(json.dumps(parser2.to_contract().to_dict(), indent=4)+'\n')
sys.exit(0)
parser.add_argument("--emit-tool-contract",
nargs=0,
action=EmitToolContractAction)
return parser
def get_contract_parser():
"""
Used to generate emitted tool contract, but not (yet) to actually process
command-line options.
"""
driver_exe = "variantCaller --resolved-tool-contract "
p = get_pbparser(
"genomic_consensus.tasks.summarize_consensus",
__VERSION__,
"Summarize Consensus",
__doc__,
Constants.DRIVER_EXE)
p.add_input_file_type(FileTypes.GFF, "alignment_summary",
"Alignment summary GFF", "Alignment summary GFF file")
p.add_input_file_type(FileTypes.GFF, "variants",
"Variants GFF", "Variants GFF file")
p.add_output_file_type(FileTypes.GFF, "output",
name="Output GFF file",
description="New alignment summary GFF file",
default_name="alignment_summary_variants.gff")
return p
def get_args_from_resolved_tool_contract(resolved_tool_contract):
rtc = resolved_tool_contract
p = get_argument_parser()
args = [
rtc.task.input_files[0],
"--variantsGff", rtc.task.input_files[1],
"--output", rtc.task.output_files[0],
]
return p.parse_args(args)
def run(options):
headers = [
("source", "GenomicConsensus %s" % __VERSION__),
("pacbio-alignment-summary-version", "0.6"),
("source-commandline", " ".join(sys.argv)),
]
inputVariantsGff = GffReader(options.variantsGff)
inputAlignmentSummaryGff = GffReader(options.inputAlignmentSummaryGff)
summaries = {}
for gffRecord in inputAlignmentSummaryGff:
region = Region(gffRecord.seqid, gffRecord.start, gffRecord.end)
summaries[region] = { "ins" : 0,
"del" : 0,
"sub" : 0,
"cQv" : (0, 0, 0)
}
inputAlignmentSummaryGff.close()
counterNames = { "insertion" : "ins",
"deletion" : "del",
"substitution" : "sub" }
for variantGffRecord in inputVariantsGff:
for region in summaries:
summary = summaries[region]
if (region.seqid == variantGffRecord.seqid and
region.start <= variantGffRecord.start <= region.end):
counterName = counterNames[variantGffRecord.type]
variantLength = max(len(variantGffRecord.reference),
len(variantGffRecord.variantSeq))
summary[counterName] += variantLength
# TODO: base consensusQV on effective coverage
summary["cQv"] = (20, 20, 20)
inputAlignmentSummaryGff = open(options.inputAlignmentSummaryGff)
outputAlignmentSummaryGff = open(options.output, "w")
inHeader = True
for line in inputAlignmentSummaryGff:
line = line.rstrip()
# Pass any metadata line straight through
if line[0] == "#":
print >>outputAlignmentSummaryGff, line.strip()
continue
if inHeader:
# We are at the end of the header -- write the tool-specific headers
for k, v in headers:
print >>outputAlignmentSummaryGff, ("##%s %s" % (k, v))
inHeader = False
# Parse the line
rec = Gff3Record.fromString(line)
if rec.type == "region":
summary = summaries[(rec.seqid, rec.start, rec.end)]
if "cQv" in summary:
cQvTuple = summary["cQv"]
line += ";%s=%s" % ("cQv", ",".join(str(int(f)) for f in cQvTuple))
for counterName in counterNames.values():
if counterName in summary:
line += ";%s=%d" % (counterName, summary[counterName])
print >>outputAlignmentSummaryGff, line
return 0
def args_runner(args):
return run(options=args)
def resolved_tool_contract_runner(resolved_tool_contract):
args = get_args_from_resolved_tool_contract(resolved_tool_contract)
return run(options=args)
def main(argv=sys.argv):
logging.basicConfig(level=logging.WARN)
mp = get_argument_parser()
log = logging.getLogger()
def dummy_log(*args, **kwargs):
pass
return pacbio_args_or_contract_runner(argv[1:],
mp,
args_runner,
resolved_tool_contract_runner,
log,
dummy_log)
if __name__ == "__main__":
sys.exit(main())
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