/
ReadLengthSep.py
executable file
·75 lines (60 loc) · 2 KB
/
ReadLengthSep.py
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#!/usr/bin/env python3
# !/bin/sh
from collections import defaultdict
import re
import os
import textwrap
import argparse
import sys
parser = argparse.ArgumentParser(
prog="SeqLengthSep.py",
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''
*******************************************************
*******************************************************
*******************************************************
Script for segregating a file into two by read length
Developed by Arkadiy Garber: agarber4@asu.edu
*******************************************************
*******************************************************
*******************************************************
'''))
parser.add_argument('-reads', type=str, help='File with sequences in FASTA format')
parser.add_argument('-long', type=str, help="output file for long reads")
parser.add_argument('-short', type=str, help="output file for short reads")
parser.add_argument('-len', type=str, help="max read length for short-reads file (default=600)", default=600)
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(0)
args = parser.parse_known_args()[0]
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:]
seq = ''
else:
header = i[1:]
seq = ''
else:
seq += i
Dict[header] = seq
return Dict
file = open(args.reads, "r")
file = fasta(file)
long = open(args.long, "w")
short = open(args.short, "w")
for i in file.keys():
if len(file[i]) > int(args.len):
long.write(">" + i + "\n")
long.write(file[i] + "\n")
else:
short.write(">" + i + "\n")
short.write(file[i] + "\n")
long.close()
short.close()