Mercurial > repos > davidvanzessen > sff_extract_demultiplex

comparison trim.py @ 3:423d320bc1ba draft default tip

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Uploaded
author davidvanzessen
date Mon, 13 Mar 2017 05:52:29 -0400
parents cb08a27e5fc2
children
comparison
equal deleted inserted replaced
2:44ec2a1009fc 3:423d320bc1ba
20 import shutil 20 import shutil
21 shutil.copy(args.input, args.output) 21 shutil.copy(args.input, args.output)
22 import sys 22 import sys
23 sys.exit() 23 sys.exit()
24 24
25 25 def trim(string, s, e):
26 if e == 0:
27 return string[s:]
28 else:
29 return string[s:-e]
26 30
27 currentSeq = "" 31 currentSeq = ""
28 currentId = "" 32 currentId = ""
29 33 with open(args.input, 'r') as i, open(args.output, 'w') as o:
30 if end is 0: 34 for line in i:
31 with open(args.input, 'r') as i: 35 print "ID:", currentId
32 with open(args.output, 'w') as o: 36 if line[0] == ">":
33 for line in i.readlines(): 37 currentSeq = trim(currentSeq, start, end)
34 if line[0] is ">": 38 if len(currentId) > 0 and len(currentSeq) > 0:
35 currentSeq = currentSeq[start:] 39 o.write(currentId)
36 if currentSeq is not "" and currentId is not "": 40 o.write(currentSeq + "\n")
37 o.write(currentId) 41 currentId = line
38 o.write(currentSeq + "\n") 42 currentSeq = ""
39 currentId = line 43 else:
40 currentSeq = "" 44 currentSeq += line.rstrip()
41 else: 45 o.write(currentId)
42 currentSeq += line.rstrip() 46 o.write(currentSeq + "\n")
43 o.write(currentId)
44 o.write(currentSeq[start:] + "\n")
45 else:
46 with open(args.input, 'r') as i:
47 with open(args.output, 'w') as o:
48 for line in i.readlines():
49 if line[0] is ">":
50 currentSeq = currentSeq[start:-end]
51 if currentSeq is not "" and currentId is not "":
52 o.write(currentId)
53 o.write(currentSeq + "\n")
54 currentId = line
55 currentSeq = ""
56 else:
57 currentSeq += line.rstrip()
58 o.write(currentId)
59 o.write(currentSeq[start:-end] + "\n")