annotate blast_unmatched.py @ 4:caa54ff096c8 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 3dcf4e7314dd6a4fefcd721ac58c8130dd1da2a1"

#!/usr/bin/env python3

import optparse
import re


def parse_options():
    """
    Parse the options guiven to the script
    """
    parser = optparse.OptionParser(description='Get unmatched blast queries')
    parser.add_option('-f', '--fasta', dest='fasta_file',
                      help='Query fasta file used during blast')
    parser.add_option('-b', '--blast', dest='blast_file',
                      help='Blast tabular output (queries in 1rst column)')
    parser.add_option('-o', '--output', dest='output_file',
                      help='Output file name')
    (options, args) = parser.parse_args()
    if len(args) > 0:
        parser.error('Wrong number of arguments')
    return options


def get_matched(blast_file):
    """
    Get a dictionary of all the queries that got a match
    """
    matched = dict()
    with open(blast_file, 'r') as infile:
        for line in infile:
            fields = line.split("\t")
            query_id = fields[0]
            matched[query_id] = 1
    return matched


def get_unmatched(output_file, fasta_file, matched):
    """
    Compares matched queries to query fasta file and print unmatched to ouput
    """
    output_file_handle = open(output_file, 'w')
    unmatched = False
    end = re.compile(r".+\W$")
    with open(fasta_file, 'r') as infile:
        for line in infile:
            if line.startswith('>'):
                subline = line[1:].rstrip()  # qid are 100chars long in blast
                if end.match(subline) is not None:
                    subline = subline[:-1]
                if subline not in matched:
                    output_file_handle.write(line)
                    unmatched = True
                else:
                    unmatched = False
            elif unmatched:
                output_file_handle.write(line)
    output_file_handle.close()


def __main__():
    opts = parse_options()
    matched = get_matched(opts.blast_file)
    get_unmatched(opts.output_file, opts.fasta_file, matched)


if __main__():
    __main__()