Mercurial > repos > yating-l > snap

comparison gff2Togff3.py @ 19:a7f57cf408e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit ff6c810cf2b46e59b45738700e68431743e4b83d
author yating-l
date Fri, 12 Aug 2016 12:03:46 -0400
parents
children 211c9b3a5c15
comparison
equal deleted inserted replaced
18:1debdbe657cd 19:a7f57cf408e8
1
2 from Group import Group
3
4 class Convertor:
5 def __init__(self, input, output):
6 with open(input) as self.f:
7 self.li = [line.rstrip().split("\t") for line in self.f]
8 self.gff3 = open(output, "w")
9 self.gff3.write("##gff-version 3\n")
10
11 def convert(self):
12 index = 0
13 while index in range(0, len(self.li)):
14 index = self.groupAsgene(index)
15 self.gff3.close()
16
17
18 def groupAsgene(self, start = 0):
19 gene = self.li[start][8]
20 index = len(self.li)
21 for i in range(start+1, len(self.li)):
22 line = self.li[i]
23 if gene != line[8]:
24 index = i
25 break
26 if index >= len(self.li):
27 group = self.li[start:len(self.li)]
28 else:
29 group = self.li[start:index]
30 g = Group(group)
31 g.writer(self.gff3)
32 return index
33
34
35
36
37 if __name__ == "__main__":
38 file = Convertor("dbia3.gff", "test.txt")
39 file.convert()
40
41
42