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# Source code for samsifter.tools.filter_ref_identity

    #!/usr/bin/env python3
    # -*- coding: utf-8 -*-
    """Filters references by identity values of assigned reads.

    This filter processes reference accessions with too few or too many reads of
    high or low percent identity in MALT'ed SAM files.

    .. 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_float_max100, check_sam)
    from samsifter.util.sam import reconstruct
    from samsifter.util.genetics import aln_identity
    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 references by % identity"
    DESC = ("Filters reference accessions with too few/many reads of high/low "
            "percent identity in MALT'ed SAM files")

    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. reads",
            desc="minimum percentage of reads with insufficient identity [50.0]",
            cli_name="--min_reads",
            default=50.0,
            unit="%",
            required=True,
            active=True
        ))

        item.add_parameter(FilterThreshold(
            text="max. reads",
            desc="maximum percentage of reads with insufficient identity [100.0]",
            cli_name="--max_reads",
            default=100.0,
            unit="%"
        ))

        item.add_parameter(FilterThreshold(
            text="min. identity",
            desc="minimum percent identity [90.0]",
            cli_name="--min_identity",
            default=90.0,
            unit="%",
            required=True,
            active=True
        ))

        item.add_parameter(FilterThreshold(
            text="max. identity",
            desc="maximum percent identity [100.0]",
            cli_name="--max_identity",
            default=100.0,
            unit="%"
        ))

        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

    def main():
        """Executable to filter SAM files for references with low identity 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)

        # thresholds for filtering
        threshold_options = parser.add_argument_group(
            title="filtering thresholds",
            description="modify cutoffs for percent identity filtering"
        )
        threshold_options.add_argument("--min_reads",
                                       action="store",
                                       type=check_pos_float_max100,
                                       dest="min_reads",
                                       help="minimum percentage of reads with \
                                       insufficient identity [50.0]",
                                       default=50.0)
        threshold_options.add_argument("--max_reads",
                                       action="store",
                                       type=check_pos_float_max100,
                                       dest="max_reads",
                                       help="maximum percentage of reads with \
                                       insufficient identity [100.0]",
                                       default=100.0)
        threshold_options.add_argument("--min_identity",
                                       action="store",
                                       type=check_pos_float_max100,
                                       dest="min_identity",
                                       help="minimum percent identity [90.0]",
                                       default=90.0)
        threshold_options.add_argument("--max_identity",
                                       action="store",
                                       type=check_pos_float_max100,
                                       dest="max_identity",
                                       help="maximum percent identity [100.0]",
                                       default=100.0)

        # options to modify calculation of percent identity
        perc_id_options = parser.add_argument_group(
            title="percent identity",
            description=("Options to modify calculation of percent identity. "
                         "Setting all three options will calculate values similar "
                         "to PMDtools, while the default settings calculate "
                         "values similar to MALT."))
        perc_id_options.add_argument("--no_deamination",
                                     action="store_true",
                                     dest="no_deamination",
                                     help="do not treat possibly deaminated T>C \
                                     and A>G pairs as mismatches in calculation \
                                     of percent identity",
                                     default=False)
        perc_id_options.add_argument("--no_indels",
                                     action="store_true",
                                     dest="no_indels",
                                     help="do not treat insertions and deletions \
                                     in alignment as mismatches in calculation of \
                                     percent identity",
                                     default=False)
        perc_id_options.add_argument("--no_unknown",
                                     action="store_true",
                                     dest="no_unknown",
                                     help="do not treat Ns in alignment as \
                                     mismatch in calculation of percent identity",
                                     default=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',
                            required=False,
                            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')

        (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")

        # exclude senseless threshold combinations
        if ((args.min_reads >= args.max_reads)
           or (args.min_identity >= args.max_identity)):
            log.error("Filter thresholds too restrictive.")
            exit(1)

        # initialize dicts and variables
        header = []      # SAM header lines, unmodified
        filtered_counts = {}    # dict of list of ints: [passed, failed]
        positions = {}   # dict of list for references 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 identity.")

        # parse SAM file and filter reads by identity thresholds
        log.info("STEP 1: parsing SAM records and determining reads with"
                 " %.1f%% <= identity <= %.1f%%"
                 % (args.min_identity, args.max_identity))
        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)

                # assuming that headers always precede alignments (SAMv1)
                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     description
                    ===========================
                    0   QNAME
                    1   FLAG
                    2   RNAME
                    3   POS
                    4   MAPQ
                    5   CIGAR
                    6   RNEXT
                    7   PNEXT
                    8   TLEN
                    9   SEQ
                    10  QUAL
                    ...optional fields...
                    11  AS          alignment score
                    12  NM          edit distance to reference
                    13  ZL          reference length
                    14  ZR          "raw score"
                    15  ZE          "expected"
                    16  ZI          percent identify (incl. indels & deaminated)
                    17  MD          mismatching positions
                    18  NS          PMD score
                    """

                    # extract accession from required RNAME field
                    # (as written by MALT 0.0.3)
                    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 = "unknown"
                        log.warn("no accession in line %s, assigning read to "
                                 "accession 'unknown'" % (line_nr + 1))

                    cigar = fields[5]
                    read = fields[9]

                    try:
                        md = line.split('MD:Z:')[1].split()[0].rstrip('\n')
                    except IndexError:
                        log.error("no MD tag in line %s" % (line_nr + 1))
                        exit(1)

                    # recreate alignment
                    (ref_full, read_full, ref_aln, read_aln) = reconstruct(read,
                                                                           cigar,
                                                                           md,
                                                                           False)

                    # calculate identity of alignment
                    # (PMD method, uses inverted defaults)
                    include_indels = not args.no_indels
                    include_deamination = not args.no_deamination
                    include_unknown = not args.no_unknown
                    (identity, mm_string) = aln_identity(read_aln,
                                                         ref_aln,
                                                         include_indels,
                                                         include_deamination,
                                                         include_unknown)

                    # filter alignment, count results
                    if ((args.min_identity <= identity * 100)
                       and (identity * 100 <= args.max_identity)):
                        # passed
                        try:
                            filtered_counts[accession][0] += 1
                        except KeyError:
                            filtered_counts[accession] = [1, 0]
                    else:
                        # failed
                        try:
                            filtered_counts[accession][1] += 1
                        except KeyError:
                            filtered_counts[accession] = [0, 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 accessions by read thresholds
        log.info("STEP 2: determining accessions with "
                 "%.1f%% <= filtered reads <= %.1f%%"
                 % (args.min_reads, args.max_reads))
        lines = []
        for accession, (passed, failed) in filtered_counts.items():
            fraction = failed / (failed + passed)
            if args.debug:
                print(failed, passed, failed + passed, fraction, file=sys.stderr)
            if ((args.min_reads <= fraction * 100.0)
               and (fraction * 100.0 <= args.max_reads)):
                lines.extend(positions[accession])
                if args.debug:
                    log.info("filtering accession: %s" % (accession,))

        # 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 accessions from SAM file
        alt = ["discarding", "keeping"]
        log.info("STEP 3: %s %i references 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 reads by identity.")

        exit()

    if __name__ == "__main__":
        main()

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