/
binning-results.py
executable file
·74 lines (46 loc) · 1.39 KB
/
binning-results.py
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#!/usr/bin/env python3
from collections import defaultdict
import re, os
import textwrap
import argparse
import sys
parser = argparse.ArgumentParser(
prog="binning-results.py",
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''
Script for summarizing into a tab-delimited file binning results
Developed by Arkadiy Garber: agarber4@asu.edu
'''))
parser.add_argument('-dir', help='directory of FASTA files')
parser.add_argument('-out', help="output table")
parser.add_argument('-x', help="extension for fasta file")
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
dir = os.listdir(args.dir)
out = open(args.out, "w")
for i in dir:
if re.findall(args.x, i):
file = open(args.dir + "/" + i, "r")
file = fasta(file)
for j in file.keys():
out.write(j + "\t" + i + "\n")