### Navigation

- index
- modules |
- SamSifter 0.5.6 documentation »
- Module code »

# Source code for samsifter.tools.filter_taxon_list

    #!/usr/bin/env python3
    # -*- coding: utf-8 -*-
    """Filter SAM files for a list of taxon IDs.

    .. 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 fileinput
    import csv
    from os.path import basename, splitext

    """ custom libraries """
    from samsifter.models.filter import FilterItem
    from samsifter.models.parameter import FilterSwitch, FilterFilepath
    from samsifter.util.arg_sanitation import check_sam, check_csv
    from samsifter.util.filters import pattern_filter

    """ global variables """
    TEXT = "Filter taxa by list of taxon IDs"
    DESC = ("filtering references by a list of NCBI taxon IDs given in a "
            "tab-separated CSV 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)
        item.set_command(splitext(basename(__file__))[0])

        item.add_parameter(FilterFilepath(
            text="taxon list file",
            desc="tab-separated CSV file with NCBI taxon IDs in first column",
            cli_name="--list",
            default="taxa.csv",
            extensions=['csv'],
            required=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"]
        ))

        return item

    def main():
        """Executable to filter SAM files for a list of taxon IDs.

        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('-l', '--list',
                            type=check_csv,
                            help="tab-separated CSV file with accession numbers "
                            "in first column",
                            required=True)
        parser.add_argument('--discard',
                            type=int,
                            help="keep or discard entries passing the filter "
                                 "criteria?",
                            required=False,
                            default=0)
        (args, remainArgs) = parser.parse_known_args()

        # generate pattern list from CSV file
        patterns = []
        with open(args.list, newline='') as csvfile:
            reader = csv.reader(csvfile, delimiter='\t')
            for row in reader:
                patterns.append("tax|" + row[0] + "|")

        # open SAM file from either command line argument or STDIN
        if args.input:
            handle = open(args.input, 'r')
        else:
            handle = fileinput.input(remainArgs)

        pattern_filter(patterns, handle, discard=(args.discard == 0))
        handle.close()

        exit()

    if __name__ == "__main__":
        main()

### Navigation

- index
- modules |
- SamSifter 0.5.6 documentation »
- Module code »