filter-fasta-seq.py

#!/usr/bin/env python3
# !/bin/sh
from collections import defaultdict
import re
import os
import textwrap
import argparse
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 allButTheLast(iterable, delim):
    x = []
    length = len(iterable.split(delim))
    for i in range(0, length-1):
        x.append(iterable.split(delim)[i])
    return iterable.join(x)


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, item):
    emptyList = []
    for i in stringOrlist:
        if i != item:
            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="filter-fasta-seq.py",
    formatter_class=argparse.RawDescriptionHelpFormatter,
    description=textwrap.dedent('''
    ************************************************************************
    Developed by Arkadiy Garber; University of Montana, Biological Sciences
    Please send comments and inquiries to rkdgarber@gmail.com
    ************************************************************************
    '''))


parser.add_argument('-f', type=str, help="input FASTA sequence file")

parser.add_argument('-o', type=str, help="output filtered FASTA file")

parser.add_argument('-r', type=str, help="comma-separated list of items to remove from FASTA file")

if len(sys.argv) == 1:
    parser.print_help(sys.stderr)
    sys.exit(0)

args = parser.parse_known_args()[0]

file = open(args.f)
file = fasta(file)
out = open(args.o, "w")


filterItems = args.r
filterList = filterItems.split(",")
for i in file.keys():
    out.write(">" + i + "\n")
    seq = removeLS(file[i], filterList)
    out.write("".join(seq) + "\n")
out.close()