/
de-align.py
executable file
·70 lines (58 loc) · 1.58 KB
/
de-align.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 urllib.request
import ssl
from urllib.error import HTTPError
import sys
parser = argparse.ArgumentParser(
prog="de-align.py",
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''
Program for removing the dashes \'(-)\' and dots \'(.)\' generated from sequence aligners.
Developed by Arkadiy Garber: agarber4@asu.edu
'''))
parser.add_argument('-i', help='input aligned fasta file')
parser.add_argument('-o', help="output unaligned fasta file")
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(0)
args = parser.parse_known_args()[0]
def remove(stringOrlist, list):
emptyList = []
for i in stringOrlist:
if i not in list:
emptyList.append(i)
else:
pass
outString = "".join(emptyList)
return outString
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 += remove(i, ["-", "."])
Dict[header] = seq
return Dict
IN = open(args.i, "r")
IN = fasta(IN)
OUT = open(args.o, "w")
for i in IN.keys():
OUT.write(">" + i + "\n")
OUT.write(IN[i] + "\n")