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unique-seq.py
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unique-seq.py
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#!/usr/bin/env python3
from collections import defaultdict
import re, os
import textwrap
import argparse
import sys
def fasta(fasta_file):
count = 0
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
count += 1
if count % 1000000 == 0:
print(count)
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
# print(count)
return Dict
parser = argparse.ArgumentParser(
prog="unique-seq.py",
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''
Script for removing redundant/identical entries (based on header name) from FASTA file
Developed by Arkadiy Garber: agarber4@asu.edu
'''))
parser.add_argument('-i', help='input fasta file')
parser.add_argument('-o', help="output fasta file")
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(0)
args = parser.parse_known_args()[0]
if args.i == args.o:
print("Input and output file names identical. Please choose a different name for output file")
raise SystemExit
file = open(args.i)
file = fasta(file)
out = open(args.o, "w")
for i in file.keys():
out.write(">" + i + "\n")
out.write(file[i] + "\n")
out.close()