Mercurial > repos > yating-l > snap

comparison gff2Togff3.py @ 0:57299471d6c1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
author yating-l
date Wed, 12 Apr 2017 17:37:47 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:57299471d6c1
1 import argparse
2 import sys
3 import fileinput
4 from Group import Group
5
6 def main():
7 parser = argparse.ArgumentParser(description='Get a gff file and the output gff3 file')
8 parser.add_argument('--input', help='input gff file')
9 parser.add_argument('--output', help='output gff3 file', required=True)
10 args = parser.parse_args()
11 input = args.input
12 output = args.output
13 if not sys.stdin.isatty():
14 c = Convertor(sys.stdin, output)
15 else:
16 c = Convertor(input, output)
17 c.convert()
18
19 class Convertor:
20 def __init__(self, input, output):
21 if type(input) is str:
22 with open(input) as self.f:
23 self.li = [line.rstrip().split("\t") for line in self.f]
24 else:
25 self.li = [line.rstrip().split("\t") for line in input]
26 self.gff3 = open(output, "w")
27 self.gff3.write("##gff-version 3\n")
28
29 def convert(self):
30 index = 0
31 while index in range(0, len(self.li)):
32 index = self.groupAsgene(index)
33 self.gff3.close()
34
35
36 def groupAsgene(self, start = 0):
37 gene = self.li[start][8]
38 index = len(self.li)
39 for i in range(start+1, len(self.li)):
40 line = self.li[i]
41 if gene != line[8]:
42 index = i
43 break
44 if index >= len(self.li):
45 group = self.li[start:len(self.li)]
46 else:
47 group = self.li[start:index]
48 g = Group(group)
49 g.writer(self.gff3)
50 return index
51
52
53
54
55 if __name__ == "__main__":
56 main()
57
58
59