Take a list of FastA files (or just one file) and count the length of the chromosome

get_chromosome_length.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# vim:fenc=utf-8 tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# Copyright © Mike Dacre <[email protected]>
#
# Distributed under terms of the MIT license
"""
#====================================================================================
#
#          FILE: get_chromosome_length (python 3)
#        AUTHOR: Michael D Dacre, [email protected]
#  ORGANIZATION: Stanford University
#       LICENSE: MIT License, Property of Stanford, Use as you wish
#       VERSION: 0.1
#       CREATED: 2014-07-21 13:26
# Last modified: 2014-07-21 13:49
#
#   DESCRIPTION: Take a FastA file and count the length of the genome
#
#====================================================================================
"""
from re import sub
from collections import OrderedDict

def count_fasta(file_list):
    """ File list is an array """
    current_chr = ''
    chromosomes = {}
    c = 0
    for genome_file in file_list:
        with open(genome_file) as infile:
            for line in infile:
                if line.startswith('>'):
                    if c:
                        chromosomes[current_chr] = str(c)
                        c = 0
                    current_chr = sub(r'^>', '', line.rstrip())
                else:
                    c = c + len(line.rstrip())
            if c:
                chromosomes[current_chr] = str(c)
    return(chromosomes)

def _get_args():
    """Command Line Argument Parsing"""
    import argparse, sys

    parser = argparse.ArgumentParser(
                 description=__doc__,
                 formatter_class=argparse.RawDescriptionHelpFormatter)

    # Required Files
    parser.add_argument('fasta_files', nargs='+',
                        help="FastA files")

    return parser

# Main function for direct running
def main():
    """Run directly"""
    # Get commandline arguments
    parser = _get_args()
    args = parser.parse_args()

    chromosomes = OrderedDict(sorted(count_fasta(args.fasta_files).items()))

    for k, v in chromosomes.items():
        print(k, v, sep='\t')

# The end
if __name__ == '__main__':
    main()