/
GC-calc.py
executable file
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/
GC-calc.py
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#!/usr/bin/env python3
# !/bin/sh
# Author: Arkadiy Garber
from collections import defaultdict
import re
import os
import textwrap
import argparse
import sys
parser = argparse.ArgumentParser(
prog="GC-calc.py",
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''
Script for calculating GC content from FASTA files
Developed by Arkadiy Garber: agarber4@asu.edu
'''))
parser.add_argument('-g', help='FASTA file input (must be nucleotide genes or contigs)')
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(0)
args = parser.parse_known_args()[0]
def lastItem(string, delim):
x = ''
ls = string.split(delim)
for i in ls:
x = i
return x
def fasta(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[header] = seq
header = i[1:]
header = header.split(" ")[0]
seq = ''
else:
header = i[1:]
header = header.split(" ")[0]
seq = ''
else:
seq += i
Dict[header] = seq
return Dict
genome = open(args.g, "r")
genome = fasta(genome)
GC = 0
total = 0
for i in genome.keys():
seq = genome[i]
total += len(seq)
gc = 0
for bp in seq:
if bp == "C" or bp == "G":
GC += 1
gc += 1
print(i + "\t" + str(round(float(GC/total), 3)))
print("------------------------------------")
print(lastItem(args.g, "/") + "\t" + str(round(float(GC/total), 3)))