ORFS-to-GFF.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 = []
    count = 0
    length = len(iterable.split(delim))
    for i in range(0, length):
        count += 1
        x.append(iterable.split(delim)[i])
        if count == length:
            x.append(delim)
    return delim.join(x[0:len(x)-2])


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:]
                seq = ''
            else:
                header = i[1:]
                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="ORFS-to-BED.py",
    formatter_class=argparse.RawDescriptionHelpFormatter,
    description=textwrap.dedent('''
    *******************************************************

    Script for generating a GFF format file from gene-calls that were created with Prodigal
    Developed by Arkadiy Garber: agarber4@asu.edu

    *******************************************************
    '''))

parser.add_argument('-orfs', type=str, help='FASTA files of ORFs that is created by Prodigal')

parser.add_argument('-gff', type=str, help="outfile in GFF format")

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

args = parser.parse_known_args()[0]

orfs = open(args.orfs)
out = open(args.gff, "w")
for i in orfs:
    if re.match(r'^>', i):
        ls = i[1:].split(" # ")
        if ls[3] == "1":
            strand = "+"
        elif ls[3] == "-1":
            strand = "-"
        out.write(allButTheLast(ls[0], "_") + "\t" + "Prodigal" + "\t" + "CDS" + "\t" + ls[1] + "\t" + ls[2] + "\t" + "." + "\t" + strand + "\t" + "0" + "\t" + "ID=" + ls[0] + "\n")
out.close()