annotate blast_unmatched.py @ 1:50c1fa95a076 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit be082f72c8d8c1eebe3f5643da1a73ab0ac9e4b3

#!/usr/bin/env python3

import optparse


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
    with open(fasta_file, 'r') as infile:
        for line in infile:
            if line.startswith('>'):
                subline = line[1:100].rstrip() #qid are 100chars long in blast
                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__()