-
Notifications
You must be signed in to change notification settings - Fork 0
/
gtfpos.py
39 lines (32 loc) · 1.04 KB
/
gtfpos.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
#!/bin/python
def lineFormat(line):
fields=line.replace(";","\t").replace(" ","\t").replace("\"","").replace(";","").strip().split('\t');
return fields;
directory="/Users/fatma/Downloads/"
outputFile=open(directory+"exonsInAGene.txt","w")
file=open(directory+"f","r")
line=file.readline()
fields=line.split('\t')
prevLine=line
prevFields=fields
while len(line) != 0:
start = fields[1]
end = fields[2]
if fields[3] == prevFields[3]:
while prevFields[3] == fields[3]:
if int(fields[1]) < int(prevFields[1]):
start = fields[1]
if int(fields[2]) > int(prevFields[2]):
end = fields[2]
prevFields=fields
line=file.readline();
if line != "":
fields=line.split('\t')
else:
break;
outputFile.write(prevFields[0] + '\t' + start + '\t' + end + '\t' + prevFields[3] + '\t' + prevFields[4])
prevFields=fields
prevLine=line
line=file.readline()
fields=line.split('\t')
outputFile.close()