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# Source code for samsifter.tools.count_taxon_reads

    #!/usr/bin/env python3
    # -*- coding: utf-8 -*-
    """Analysing filter step to count reads per taxon.

    .. 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
    from os.path import basename, splitext, isfile

    """ custom libraries """
    from samsifter.models.filter import FilterItem
    from samsifter.models.parameter import FilterParameter, FilterFilepath
    from samsifter.util.arg_sanitation import check_sam

    """ global variables """
    TEXT = "Count reads per taxon"
    DESC = ("Counts reads per taxon ID and stores them in a separate statistics "
            "file.")

    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, icon=FilterItem.ICON_ANALYZER)
        item.set_command(splitext(basename(__file__))[0])

        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(FilterFilepath(
            text="prefix",
            desc="prefix of temporary statistics files",
            cli_name="--prefix",
            default='${filename}',  # crucial for clean batch processing!
            active=True
        ))

        # input/output requirements
        item.set_input_format('SAM')
        item.set_input_sorting('any')
        item.set_input_compression('uncompressed')
        item.set_output_format('SAM')
        item.set_output_sorting('as_input')
        item.set_output_compression('uncompressed')

        return item

    def main():
        # 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('-p', '--prefix',
                            required=False,
                            default='reads_per_taxon',
                            help='prefix of temporary statistics files')
        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')
        (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")

        log.info("START of counting reads per taxon.")

        # initialize dict
        counts = {}

        # parse SAM file
        log.info("STEP 1: parsing SAM records.")
        try:
            # open SAM file from either command line argument or STDIN
            if args.input:
                handle = open(args.input, 'r')
            else:
                handle = fileinput.input(remainArgs)

            for line_nr, line in enumerate(handle, 1):
                if not line.startswith("@"):
                    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 taxon ID 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
                    """

                    try:
                        taxon_id = rname_parts[5]
                    except IndexError:
                        taxon_id = 'unknown'
                        log.warn("no taxon ID in line %s, assigning read to "
                                 "taxon 'unknown'" % line_nr)

                    # add to counts
                    try:
                        counts[taxon_id] += 1
                    except KeyError:
                        counts[taxon_id] = 1

                print(line.rstrip(), file=sys.stdout)

        finally:
            handle.close()

        # check if previous statistic files exist and choose filename accordingly
        suffix = 'csv'
        # assuming that 999 filter steps will suffice
        for idx in range(1, 1000):
            stats_filename = '%s.%03d.%s' % (args.prefix, idx, suffix)
            if not isfile(stats_filename):
                break

        log.info("STEP 2: writing statistics to %s." % stats_filename)
        with open(stats_filename, mode='w') as handle:
            print("'taxon_id','read_count'", file=handle)
            for k, v in sorted(counts.items()):
                print("'%s',%i" % (k, v), file=handle)

        log.info("END of counting reads per taxon.")

        exit()

    if __name__ == "__main__":
        main()

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