parse_big_fasta.py

"""
Parses RVDB formatted FASTA headers so they can be interperated by
HIVE-hexagon's tablequery

Input:
#######
    * -i : input FASTA file to reformat

    * -o : specified output file

Output:
#######
    * Reformatted FASTA file

Usage:
#######

    *python parse_big_fasta.py --version

    *This is the option that show you the program's version.*

    *python parse_big_fasta.py -h

    *This can show you some help information*

    *python parse_big_fasta.py -i <filename.fasta> -o <output_file>

    *Runs program with specified FASTA file and output file*

"""
# !/usr/bin/env python
# -*- coding: utf-8 -*-

################################################################################
# parse-big-fasta.py
################################################################################

__version__ = "1.0"
__status__ = "Dev"

import re
import sys
import argparse


# ______________________________________________________________________________#
def create_arg_parser():
    """
    Creates and returns the ArgumentParser object.
    """

    parser = argparse.ArgumentParser(
        description='Fixes RVDB fasta file header format for HIVE-hexagon and tablequery.')

    parser.add_argument('-i', 'inputFASTA',
                        help='Path to the input FASTA.')

    parser.add_argument('-o', '--output',
                        help='The output file for the new FASTA. If no output is provided the '
                             'default will just append NEW to the file name')

    return parser


# ______________________________________________________________________________#
def format_header(parsed_args):
    """
    Parse the RVDB formatted FASTA headers and re-writes in desired format
    """

    accessions = []
    with open(parsed_args.inputFASTA) as infile:
        reader = infile.readlines()
        try:
            with open(parsed_args.output, 'w') as outfile:
                for line in reader:
                    if re.search('^>', line):
                        newline = line.split('|')[2:]
                        newline = '>gb|' + '|'.join(newline)
                        accessions.append(newline[0])
                        outfile.writelines(newline)
                    else:
                        outfile.writelines(line)
        except FileNotFoundError:
            outfile = 'new_' + parsed_args.inputFASTA
            with open(outfile, 'w') as outfile:
                for line in reader:
                    if re.search('^>', line):
                        newline = line.split('|')[2:]
                        accessions.append(newline[0])
                        newline = '>gb|' + '|'.join(newline)
                        outfile.writelines(newline)
                    else:
                        outfile.writelines(line)

    return accessions


# ______________________________________________________________________________#

def main():
    """
    Write reformatted .fasta to specified file
    """
    arg_parser = create_arg_parser()
    parsed_args = arg_parser.parse_args(sys.argv[1:])
    accessions = format_header(parsed_args)
    print(accessions)
    with open('accessions.txt', 'w') as acc:
        for accession in accessions:
            acc.write(accession + '\n')


# ______________________________________________________________________________#
if __name__ == "__main__":
    main()