Mercurial > repos > davidvanzessen > baseline_bayesian_estimation
comparison script_imgt.py @ 5:d8de51314d3f draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 14 Aug 2014 07:17:26 -0400 |
| parents | 94fada165724 |
| children | 7eeb7b808af9 |
comparison
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| 4:1726dc8f3e0a | 5:d8de51314d3f |
|---|---|
| 12 | 12 |
| 13 refdic = dict() | 13 refdic = dict() |
| 14 with open(args.ref, 'r') as ref: | 14 with open(args.ref, 'r') as ref: |
| 15 currentSeq = "" | 15 currentSeq = "" |
| 16 currentId = "" | 16 currentId = "" |
| 17 for line in ref.readlines(): | 17 for line in ref: |
| 18 if line[0] is ">": | 18 if line[0] is ">": |
| 19 if currentSeq is not "" and currentId is not "": | 19 if currentSeq is not "" and currentId is not "": |
| 20 refdic[currentId[1:]] = currentSeq | 20 refdic[currentId[1:]] = currentSeq |
| 21 currentId = line.rstrip() | 21 currentId = line.rstrip() |
| 22 currentSeq = "" | 22 currentSeq = "" |
| 46 | 46 |
| 47 | 47 |
| 48 | 48 |
| 49 currentSeq = "" | 49 currentSeq = "" |
| 50 currentId = "" | 50 currentId = "" |
| 51 first=True | |
| 51 with open(args.input, 'r') as i: | 52 with open(args.input, 'r') as i: |
| 52 with open(args.output, 'a') as o: | 53 with open(args.output, 'a') as o: |
| 53 o.write(">>>" + args.id + "\n") | 54 o.write(">>>" + args.id + "\n") |
| 54 outputdic = dict() | 55 outputdic = dict() |
| 55 for line in i.readlines()[1:]: | 56 for line in i: |
| 57 if first: | |
| 58 first = False | |
| 59 continue | |
| 56 linesplt = line.split("\t") | 60 linesplt = line.split("\t") |
| 57 ref = filterGene(linesplt[1], vPattern) | 61 ref = filterGene(linesplt[1], vPattern) |
| 58 if not ref or not linesplt[2].rstrip(): | 62 if not ref or not linesplt[2].rstrip(): |
| 59 continue | 63 continue |
| 60 if ref in outputdic: | 64 if ref in outputdic: |