annotate cherry_pick_fasta.py @ 3:c282a8a47dd9 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Chery pick of fasta sequences satisfying a query string in their header/name
import argparse

from Bio import SeqIO


def Parser():
    the_parser = argparse.ArgumentParser(
        description='Cherry pick fasta sequences')
    the_parser.add_argument('--input', action='store', type=str,
                            help='input fasta file')
    the_parser.add_argument('--searchfor', action='store', type=str,
                            help='with, without, or withlist, withoutlist')
    the_parser.add_argument('--mode', action='store', type=str,
                            default='includes', help='exact or includes')
    the_parser.add_argument('--query-string', dest='query_string',
                            action='store', type=str,
                            help='headers containing the string will be \
                                  extracted or excluded as well as the \
                                  corresponding sequence')
    the_parser.add_argument('--query-file', dest='query_file',
                            action='store', type=str,
                            help='headers containing any of the strings \
                                  provided in the text file (1 string per \
                                  line) will be extracted or excluded as well \
                                   as the corresponding sequence')
    the_parser.add_argument('--output', action='store', type=str,
                            help='output fasta file')
    args = the_parser.parse_args()
    return args


def parse_fasta_dict(query, fasta_dict, mode):
    if not isinstance(query, list):
        query = [query]
    accumulator = []
    if mode == 'includes':
        for seq_id in fasta_dict:
            for string in query:
                if string in seq_id:
                    accumulator.append(seq_id)
                    continue
    elif mode == 'exact':
        for seq_id in fasta_dict:
            for string in query:
                if string == seq_id:
                    accumulator.append(seq_id)
                    continue
    res_dict = {k: fasta_dict[k] for k in fasta_dict if k in accumulator}
    return res_dict


def complement_fasta_dict(fasta_dict, subfasta_dict):
    fasta_ids = list(fasta_dict.keys())
    subfasta_ids = list(subfasta_dict.keys())
    complement_ids = list(set(fasta_ids) - set(subfasta_ids))
    sub_dict = {k: fasta_dict[k] for k in fasta_dict if k in complement_ids}
    return sub_dict


def getquerylist(file):
    querylist = []
    for line in open(file, 'r'):
        querylist.append(line.rstrip())
    return querylist


def buid_fasta_dict(fasta):
    seq_dict = {rec.id: rec.seq for rec in SeqIO.parse(fasta, "fasta")}
    return seq_dict


def write_fasta_result(fasta_dict, file):
    line_length = 60
    with open(file, 'w') as f:
        for header in sorted(fasta_dict):
            f.write('>%s\n' % header)
            for i in range(line_length, len(fasta_dict[header]), line_length):
                f.write('%s\n' % fasta_dict[header][i-line_length:i])
            f.write('%s\n' % fasta_dict[header][i:])


def __main__():
    ''' main function '''
    args = Parser()
    fasta_dict = buid_fasta_dict(args.input)
    if args.query_string:
        query = args.query_string
    elif args.query_file:
        query = getquerylist(args.query_file)
    if args.searchfor == 'with':
        fasta_result_dict = parse_fasta_dict(query, fasta_dict, args.mode)
    elif args.searchfor == 'without':
        fasta_result_dict = complement_fasta_dict(fasta_dict, parse_fasta_dict(
                                                  query, fasta_dict,
                                                  args.mode))
    write_fasta_result(fasta_result_dict, args.output)


if __name__ == '__main__':
    __main__()