|
0
|
1 import argparse
|
|
|
2
|
|
|
3 #docs.python.org/dev/library/argparse.html
|
|
|
4 parser = argparse.ArgumentParser()
|
|
|
5 parser.add_argument("--input", help="Input fasta")
|
|
|
6 parser.add_argument("--output", help="Output fasta")
|
|
|
7 parser.add_argument("--start", help="How many nucleotides to trim from the start", type=int)
|
|
|
8 parser.add_argument("--end", help="How many nucleotides to trim from the end", type=int)
|
|
|
9
|
|
|
10 args = parser.parse_args()
|
|
|
11 start = int(args.start)
|
|
|
12 end = int(args.end)
|
|
|
13
|
|
|
14 print args.input
|
|
|
15 print args.output
|
|
|
16 print start
|
|
|
17 print end
|
|
|
18
|
|
|
19 if end <= 0 and start <= 0:
|
|
|
20 import shutil
|
|
|
21 shutil.copy(args.input, args.output)
|
|
|
22 import sys
|
|
|
23 sys.exit()
|
|
|
24
|
|
|
25
|
|
|
26
|
|
|
27 currentSeq = ""
|
|
|
28 currentId = ""
|
|
|
29
|
|
|
30 if end is 0:
|
|
|
31 with open(args.input, 'r') as i:
|
|
|
32 with open(args.output, 'w') as o:
|
|
|
33 for line in i.readlines():
|
|
|
34 if line[0] is ">":
|
|
|
35 currentSeq = currentSeq[start:]
|
|
|
36 if currentSeq is not "" and currentId is not "":
|
|
|
37 o.write(currentId)
|
|
|
38 o.write(currentSeq + "\n")
|
|
|
39 currentId = line
|
|
|
40 currentSeq = ""
|
|
|
41 else:
|
|
|
42 currentSeq += line.rstrip()
|
|
|
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")
|
