/usr/bin/summarizeConsensus is in pbgenomicconsensus 2.1.0-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 | #!/usr/bin/python
"""
Augment the alignment_summary.gff file with consensus and variants information.
"""
from collections import namedtuple, defaultdict
import argparse
import logging
import bisect
import json
import gzip
import sys
import numpy as np
from pbcommand.utils import setup_log
from pbcommand.cli import pbparser_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"))
log = logging.getLogger(__name__)
class Constants(object):
TOOL_ID = "genomic_consensus.tasks.summarize_consensus"
DRIVER_EXE = "summarizeConsensus --resolved-tool-contract "
def get_contract_parser():
p = get_pbparser(
Constants.TOOL_ID,
__VERSION__,
"Summarize Consensus",
__doc__,
Constants.DRIVER_EXE,
default_level="ERROR")
p.add_input_file_type(FileTypes.GFF, "alignment_summary",
"Alignment summary GFF", "Alignment summary GFF file")
p.tool_contract_parser.add_input_file_type(FileTypes.GFF, "variants",
"Variants GFF", "Variants GFF file")
p.arg_parser.parser.add_argument("--variantsGff",
type=str,
help="Input variants.gff or variants.gff.gz filename",
required=True)
p.tool_contract_parser.add_output_file_type(FileTypes.GFF, "output",
name="Output GFF file",
description="New alignment summary GFF file",
default_name="alignment_summary_variants")
p.arg_parser.parser.add_argument("-o", "--output",
type=str,
help="Output alignment_summary.gff filename")
return p
def get_args_from_resolved_tool_contract(resolved_tool_contract):
rtc = resolved_tool_contract
p = get_contract_parser().arg_parser.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.alignment_summary)
summaries = {}
for gffRecord in inputAlignmentSummaryGff:
region = Region(gffRecord.seqid, gffRecord.start, gffRecord.end)
summaries[region] = { "ins" : 0,
"del" : 0,
"sub" : 0,
# TODO: base consensusQV on effective coverage
"cQv" : (20, 20, 20)
}
inputAlignmentSummaryGff.close()
counterNames = { "insertion" : "ins",
"deletion" : "del",
"substitution" : "sub" }
regions_by_contig = defaultdict(list)
for region in summaries:
regions_by_contig[region.seqid].append(region)
for seqid in regions_by_contig.keys():
r = regions_by_contig[seqid]
regions_by_contig[seqid] = sorted(r, lambda a,b: cmp(a.start, b.start))
logging.info("Processing variant records")
i = 0
have_contigs = set(regions_by_contig.keys())
for variantGffRecord in inputVariantsGff:
if not variantGffRecord.seqid in have_contigs:
raise KeyError(
"Can't find alignment summary for contig '{s}".format(
s=variantGffRecord.seqid))
positions = [r.start for r in regions_by_contig[variantGffRecord.seqid]]
idx = bisect.bisect_right(positions, variantGffRecord.start) - 1
# XXX we have to be a little careful here - an insertion at the start
# of a contig will have start=0 versus start=1 for the first region
if idx < 0:
idx = 0
region = regions_by_contig[variantGffRecord.seqid][idx]
assert ((region.start <= variantGffRecord.start <= region.end) or
(region.start == 1 and variantGffRecord.start == 0 and
variantGffRecord.type == "insertion")), \
(variantGffRecord.seqid, region.start, variantGffRecord.start,
region.end, variantGffRecord.type, idx)
summary = summaries[region]
counterName = counterNames[variantGffRecord.type]
variantLength = max(len(variantGffRecord.reference),
len(variantGffRecord.variantSeq))
summary[counterName] += variantLength
i += 1
if i % 1000 == 0:
logging.info("{i} records...".format(i=i))
inputAlignmentSummaryGff = open(options.alignment_summary)
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):
return pbparser_runner(argv[1:],
get_contract_parser(),
args_runner,
resolved_tool_contract_runner,
log,
setup_log)
if __name__ == "__main__":
sys.exit(main())
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