comparison blast_unmatched.py @ 2:dfcdac284538 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 830e10a94c2afc178f4078609842cd93808df1b4

1:50c1fa95a076

#!/usr/bin/env python3

import optparse


def parse_options():
    """
    Parse the options guiven to the script
    """

    """
    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

2:dfcdac284538

#!/usr/bin/env python3

import optparse
import re

def parse_options():
    """
    Parse the options guiven to the script
    """

    """
    Compares matched queries to query fasta file and print unmatched to ouput
    """
    output_file_handle = open(output_file, 'w')
    unmatched = False
    end = re.compile(".+\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
                while end.match(subline) != None:
                    subline = subline[:-1]
                if subline not in matched:
                    output_file_handle.write(line)
                    unmatched = True
                else:
                    unmatched = False