Source code for samsifter.tools.filter_taxon_pmds

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Filter taxa 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
from samsifter.util.papertrail import modify_header
from samsifter.version import samsifter_version

__version__ = samsifter_version

""" global variables """
TEXT = "Filter taxa 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 )) item.add_parameter(FilterParameter( text="write PG tag", desc="annotate the filtered SAM file by adding a PG tag to the header", cli_name="--modify", default=True, active=True )) return item
[docs]def main(): """Executable to filter SAM files for taxa 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('-d', '--debug', required=False, action='store_true', help='print debug messages to stderr') parser.add_argument('-m', '--modify', required=False, action='store_true', help='modify header by adding PG record') 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") # initialize dicts and variables header = [] # SAM header lines, unmodified total_read_counts = {} ancient_read_counts = {} positions = {} # dict of list for taxon IDs and their line numbers buffer = None # file handle used to buffer complete STDIN byte_offset = 0 # offset of first line after end of header line_offset = 0 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("@"): if args.modify: line_offset = line_nr + 1 # store header lines for later modification header.append(line) # increase offset until reaching end of header byte_offset += len(line) 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 """ taxon_id = "" try: taxon_id = rname_parts[5] except IndexError: taxon_id = "unknown" log.warn("no taxon ID in line %i, read assigned to taxon " "'unknown'" % (line_nr + 1)) # 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 (taxon_id in total_read_counts): total_read_counts[taxon_id] += 1 else: total_read_counts[taxon_id] = 1 if (pmds >= args.pmds): if (taxon_id in ancient_read_counts): ancient_read_counts[taxon_id] += 1 else: ancient_read_counts[taxon_id] = 1 # remember occurence of taxon ID and line number(s) try: positions[taxon_id].append(line_nr) except KeyError: positions[taxon_id] = [line_nr, ] finally: handle.close() buffer.seek(0) # filter taxa log.info("STEP 2: determining taxa matching the filter criteria.") lines = [] for (taxon_id, ancientReadCount) in sorted(ancient_read_counts.items()): if args.reads_total: if (ancientReadCount >= args.reads_total): lines.extend(positions[taxon_id]) if args.debug: log.info("filtering taxon: %s" % taxon_id) elif args.reads_perc: perc = ancientReadCount / total_read_counts[taxon_id] * 100.0 if (perc >= args.reads_perc): lines.extend(positions[taxon_id]) if args.debug: log.info("filtering taxon: %s" % taxon_id) # re-open file if not a buffered stream if buffer is None: buffer = open(args.input, 'r') # skip original headers and sneak in modified headers instead if args.modify: log.info("Writing new @PG record to SAM header.") cl = " ".join(sys.argv[1:]) modified_header = modify_header( header, name=splitext(basename(__file__))[0], version=__version__, command_line=cl, description=TEXT ) extra_headers = len(modified_header) - len(header) # should be 1 for record in modified_header: print(record.rstrip(), file=sys.stdout) # fast forward buffer to beginning of alignments buffer.seek(byte_offset) if args.debug: log.info("%i new line added to header lines." % extra_headers) # keep or remove taxa from SAM file alt = ["discarding", "keeping"] log.info("STEP 3: %s %i taxa from SAM file." % (alt[args.discard], len(lines))) line_filter(lines, buffer, discard=(args.discard == 0), offset=line_offset) buffer.close() log.info("END of filtering taxa by PMDS.") exit()
if __name__ == "__main__": main()