annotate format_reago_input_files.py @ 0:13dd84cab09e draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit f5be73e67192909db96dfab214f4360eb41757a4

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

import argparse


def add_read_pair_num(input_filepath, output_filepath, read_pair_num):
    to_add = "." + str(read_pair_num)
    with open(input_filepath, "r") as input_file:
        with open(output_filepath, "w") as output_file:
            for line in input_file:
                if line.startswith(">"):
                    split_line = line.split()
                    seq_id = split_line[0]
                    if seq_id.rfind(to_add) != (len(seq_id) - len(to_add)):
                        split_line[0] = seq_id + to_add
                    output_file.write(" ".join(split_line) + "\n")
                else:
                    output_file.write(line)


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument("--r1_input", required=True)
    parser.add_argument("--r2_input", required=True)
    parser.add_argument("--r1_output", required=True)
    parser.add_argument("--r2_output", required=True)
    args = parser.parse_args()

    add_read_pair_num(args.r1_input, args.r1_output, 1)
    add_read_pair_num(args.r2_input, args.r2_output, 2)