annotate scripts/S05_find_rbh.py @ 0:90b57ab0bd1d draft default tip

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty

#!/usr/bin/env python
# coding: utf-8
# Author : Victor Mataigne

import argparse, pickle, itertools

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('besthits_file1', help='')
    parser.add_argument('besthits_file2', help='')
    args = parser.parse_args()

    # Open dict of best hits
    file_best_hit_dict_q = open('dict_best_hits_from_blast_1')
    file_best_hit_dict_db = open('dict_best_hits_from_blast_2')
    best_hit_dict_q = pickle.load(file_best_hit_dict_q)
    best_hit_dict_db = pickle.load(file_best_hit_dict_db)
    file_best_hit_dict_q.close()
    file_best_hit_dict_db.close()    

    best_h1 = {}
    with open(args.besthits_file1, 'r') as bh1 :
        for h, s in itertools.izip_longest(*[bh1]*2):
            header = h.strip('>\n')
            sequence = s.strip('\n')
            best_h1[header] = sequence

    best_h2 = {}
    with open(args.besthits_file2, 'r') as bh2 :
        for h, s in itertools.izip_longest(*[bh2]*2):
            header = h.strip('>\n')
            sequence = s.strip('\n')
            best_h2[header] = sequence
    
    # Find RBH:
    reverse_best_hit_dict_db = dict((v,k) for k,v in best_hit_dict_db.iteritems())    

    rbh = set(best_hit_dict_q.items()).intersection(set(reverse_best_hit_dict_db.items()))

    s = args.besthits_file1.split('_')
    suffix = s[4] + '_' + s[5]
    out_name = 'RBH_{}_dna.fasta'.format(suffix)
    output = open(out_name, 'w')

    for pairwise_couple in rbh :
        output.write('>'+pairwise_couple[0]+'\n')
        output.write(best_h1[pairwise_couple[0]]+'\n')
        output.write('>'+pairwise_couple[1]+'\n')
        output.write(best_h2[pairwise_couple[1]]+'\n')
    output.close()

if __name__ == "__main__":
    main()