#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Filter references with high attribution of ancient reads in a MALT'ed and
PMD'ed SAM file
.. moduleauthor:: Florian Aldehoff <faldehoff@student.uni-tuebingen.de>
"""
import sys
if not (sys.version_info[0] >= 3):
print("Error, I need python 3.x or newer")
exit(1)
import argparse
import logging as log
import fileinput
import tempfile
from os.path import basename, splitext
""" custom libraries """
from samsifter.models.filter import FilterItem
from samsifter.models.parameter import (
FilterParameter, FilterSwitch, FilterThreshold
)
from samsifter.util.arg_sanitation import (
check_pos_int, check_sam, check_percent
)
from samsifter.util.filters import line_filter
""" global variables """
TEXT = "Filter references by PMD score"
DESC = ("Filter taxa with high attribution of ancient reads in a MALT'ed and "
"PMD'ed SAM file")
[docs]def item():
"""Create item representing this tool in list and tree views.
Returns
-------
FilterItem
Item for use in item-based list and tree views.
"""
item = FilterItem(text=TEXT, desc=DESC)
item.set_command(splitext(basename(__file__))[0])
item.add_parameter(FilterThreshold(
text="min. PMDS",
desc="minimum post-mortem degradation score (PMDS)",
cli_name="--pmds",
default=3,
minimum=-10,
maximum=10,
precision=0,
required=True,
active=True
))
item.add_parameter(FilterThreshold(
text="min. reads",
desc="minimum percentage of reads exceeding PMD threshold [50.0]",
cli_name="--reads_perc",
default=50.0,
unit="%",
required=True,
active=True
))
item.add_parameter(FilterSwitch(
text="filter direction",
desc="Keep or discard entries passing the filter criteria?",
cli_name="--discard",
default=0,
options=["discard", "keep"]
))
item.add_parameter(FilterParameter(
text="verbose",
desc="print additional information to STDERR",
cli_name="--verbose",
default=True,
active=True
))
item.add_parameter(FilterParameter(
text="debug",
desc="print debug messages to STDERR",
cli_name="--debug",
default=False
))
return item
[docs]def main():
"""Executable to filter SAM files for references with ancient reads.
See ``--help`` for details on expected arguments. Takes input from
either STDIN, or optional, or positional arguments. Logs messages to
STDERR and writes processed SAM files to STDOUT.
"""
# parse arguments
parser = argparse.ArgumentParser(description=DESC)
parser.add_argument('-i', '--input',
type=check_sam,
help="specify SAM file to be analysed (default: "
"STDIN)",
required=False)
parser.add_argument('--discard',
type=int,
help="keep or discard entries passing the filter "
"criteria?",
required=False,
default=0)
parser.add_argument('-v', '--verbose',
action='store_true',
help='print additional information to stderr')
parser.add_argument('-p', '--pmds',
required=True,
type=float,
help='post-mortem degradation score (PMDS) threshold')
read_thresholds = parser.add_mutually_exclusive_group(required=True)
read_thresholds.add_argument('-rp', '--reads_perc',
type=check_percent,
help='attributed read threshold (percent)')
read_thresholds.add_argument('-rt', '--reads_total',
type=check_pos_int,
help='attributed read threshold (total)')
(args, remainArgs) = parser.parse_known_args()
# configure logging
if args.verbose:
log.basicConfig(format="%(levelname)s: %(message)s", level=log.DEBUG)
else:
log.basicConfig(format="%(levelname)s: %(message)s")
totalReadCounts = {}
ancientReadCounts = {}
header = []
positions = {} # dict of list for references and their line numbers
buffer = None # file handle used to buffer complete STDIN
log.info("START of filtering references by PMDS.")
# parse SAM file
log.info("STEP 1: parsing SAM records.")
try:
"""
open SAM file from either command line argument or STDIN
use temporary file as buffer if reading from STDIN
"""
if args.input:
handle = open(args.input, 'r')
else:
handle = fileinput.input(remainArgs)
buffer = tempfile.TemporaryFile(mode='w+')
for line_nr, line in enumerate(handle, 0):
if buffer is not None:
buffer.write(line)
if line.startswith("@"):
header.append(line)
# TODO modify header lines for program history
else:
fields = line.split("\t")
"""
# content
====================
0 QNAME
1 FLAG
2 RNAME
3 POS
4 MAPQ
5 CIGAR
6 RNEXT
7 PNEXT
8 TLEN
9 SEQ
10 QUAL
...optional fields...
18 NS
"""
# extract taxon ID from required RNAME field (written by MALT)
rname_parts = fields[2].split("|")
"""
# content
===============
0 gi
1 GenBank ID
2 ref
3 accession
4 tax
5 taxonomy ID
"""
accession = ""
try:
accession = rname_parts[3]
except IndexError:
accession = "unspecified reference"
log.warn("no accession in line %i, run MALT version "
"0.0.3 or higher" % (line_nr, ))
# extract PMD score from optional NS field
# (written by pmdtools)
pmds = 0
try:
ns_parts = fields[18].split(":")
pmds = float(ns_parts[2])
except ValueError:
log.error("invalid PMD score in line %i: %s"
% (line_nr + 1, ns_parts[2]))
exit(1)
except IndexError:
log.error(
"no PMD score in line %i, run 'pmdtools --dry "
"--header --writesamfield' first" % (line_nr + 1))
exit(1)
# count and filter reads by PMDS
if (accession in totalReadCounts):
totalReadCounts[accession] += 1
else:
totalReadCounts[accession] = 1
if (pmds >= args.pmds):
if (accession in ancientReadCounts):
ancientReadCounts[accession] += 1
else:
ancientReadCounts[accession] = 1
# remember occurence of accession and line number(s)
try:
positions[accession].append(line_nr)
except KeyError:
positions[accession] = [line_nr, ]
finally:
handle.close()
buffer.seek(0)
# filter references
log.info("STEP 2: determining references matching the filter criteria.")
lines = []
for (accession, ancientReadCount) in sorted(ancientReadCounts.items()):
if args.reads_total:
if (ancientReadCount >= args.reads_total):
lines.extend(positions[accession])
if args.debug:
log.info("filtering accession: %s" % (accession, ))
elif args.reads_perc:
perc = ancientReadCount / totalReadCounts[accession] * 100.0
if (perc >= args.reads_perc):
lines.extend(positions[accession])
if args.debug:
log.info("filtering accession: %s" % (accession, ))
# keep or remove accessions from SAM file
alt = ["discarding", "keeping"]
log.info("STEP 3: %s %i references from SAM file." %
(alt[args.discard], len(lines)))
if buffer is None:
buffer = open(args.input, 'r')
line_filter(lines, buffer, discard=(args.discard == 0))
buffer.close()
log.info("END of filtering references by PMDS.")
exit()
if __name__ == "__main__":
main()