comparison gff2Togff3.py @ 21:211c9b3a5c15 draft

planemo upload commit 6e3286c6569d531846474dcd6959378af0317ce3-dirty

20:04e57f9ef873

from Group import Group

class Convertor:
    def __init__(self, input, output):
        with open(input) as self.f:
            self.li = [line.rstrip().split("\t") for line in self.f]
        self.gff3 = open(output, "w")
        self.gff3.write("##gff-version 3\n")

    def convert(self):
        index = 0

   
        

if __name__ == "__main__":
    file = Convertor("dbia3.gff", "test.txt")
    file.convert()


    

21:211c9b3a5c15

import argparse
import sys
import fileinput
from Group import Group

def main():
        parser = argparse.ArgumentParser(description='Get a gff file and the output gff3 file')
        parser.add_argument('--input', help='input gff file')
        parser.add_argument('--output', help='output gff3 file', required=True)
        args = parser.parse_args()
        input = args.input
        output = args.output
        if not sys.stdin.isatty():
            c = Convertor(sys.stdin, output)
        else: 
            c = Convertor(input, output)
        c.convert()
        
class Convertor:    
    def __init__(self, input, output):
        if type(input) is str:
            with open(input) as self.f:
                self.li = [line.rstrip().split("\t") for line in self.f]
        else:
            self.li = [line.rstrip().split("\t") for line in input]
        self.gff3 = open(output, "w")
        self.gff3.write("##gff-version 3\n")

    def convert(self):
        index = 0

   
        

if __name__ == "__main__":
    main()