/
fasta-filter.py
executable file
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fasta-filter.py
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#!/usr/bin/env python3
# !/bin/sh
from collections import defaultdict
import re
import os
import textwrap
import argparse
import urllib.request
import ssl
import sys
def cluster(data, maxgap):
'''Arrange data into groups where successive elements
differ by no more than *maxgap*
#->>> cluster([1, 6, 9, 100, 102, 105, 109, 134, 139], maxgap=10)
[[1, 6, 9], [100, 102, 105, 109], [134, 139]]
#->>> cluster([1, 6, 9, 99, 100, 102, 105, 134, 139, 141], maxgap=10)
[[1, 6, 9], [99, 100, 102, 105], [134, 139, 141]]
'''
# data = sorted(data)
data.sort(key=int)
groups = [[data[0]]]
for x in data[1:]:
if abs(x - groups[-1][-1]) <= maxgap:
groups[-1].append(x)
else:
groups.append([x])
return groups
def lastItem(ls):
x = ''
for i in ls:
x = i
return x
def RemoveDuplicates(ls):
empLS = []
counter = 0
for i in ls:
if i not in empLS:
empLS.append(i)
else:
pass
return empLS
def allButTheLast(iterable, delim):
x = ''
length = len(iterable.split(delim))
for i in range(0, length-1):
x += iterable.split(delim)[i]
x += delim
return x[0:len(x)-1]
def secondToLastItem(ls):
x = ''
for i in ls[0:len(ls)-1]:
x = i
return x
def pull(item, one, two):
ls = []
counter = 0
for i in item:
if counter == 0:
if i != one:
pass
else:
counter += 1
ls.append(i)
else:
if i != two:
ls.append(i)
else:
ls.append(i)
counter = 0
outstr = "".join(ls)
return outstr
def stabilityCounter(int):
if len(str(int)) == 1:
string = (str(0) + str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 2:
string = (str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 3:
string = (str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 4:
string = (str(0) + str(int))
return (string)
def replace(stringOrlist, list, item):
emptyList = []
for i in stringOrlist:
if i not in list:
emptyList.append(i)
else:
emptyList.append(item)
outString = "".join(emptyList)
return outString
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 removeLS(stringOrlist, list):
emptyList = []
for i in stringOrlist:
if i not in list:
emptyList.append(i)
else:
pass
return emptyList
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
# print(count)
return Dict
def filter(list, items):
outLS = []
for i in list:
if i not in items:
outLS.append(i)
return outLS
def delim(line):
ls = []
string = ''
for i in line:
if i != " ":
string += i
else:
ls.append(string)
string = ''
ls = filter(ls, [""])
return ls
parser = argparse.ArgumentParser(
prog="fasta-filter.py",
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''
*******************************************************
Script to selectively filter entries out of FASTA files
Developed by Arkadiy Garber: agarber4@asu.edu
*******************************************************
'''))
parser.add_argument('-f', type=str, help='fasta to filter')
parser.add_argument('-e', type=str, help='file with headers to exclude from original')
parser.add_argument('-m', type=str, help='is the file with headers to exclude in fasta format or tsv (fasta/tsv)')
parser.add_argument('-o', type=str, help="name output file")
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(0)
args = parser.parse_known_args()[0]
if args.f != args.o:
if args.m == "fasta":
exclude = open(args.e)
exclude = fasta(exclude)
file = open(args.f)
file = fasta(file)
out = open(args.o, "w")
for i in file.keys():
if i not in exclude.keys():
out.write(">" + i + "\n")
out.write(file[i] + "\n")
out.close()
else:
exclude = open(args.e)
excludeList = []
for i in exclude:
line = i.rstrip()
excludeList.append(line)
file = open(args.f)
file = fasta(file)
out = open(args.o, "w")
for i in file.keys():
if i not in excludeList:
out.write(">" + i + "\n")
out.write(file[i] + "\n")
out.close()
else:
print("output file name same as input fasta file!")
print("exiting")