Mercurial > repos > fcaramia > contra
comparison Contra/scripts/convert_targeted_regions.py @ 0:7564f3b1e675
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| author | fcaramia |
|---|---|
| date | Thu, 13 Sep 2012 02:31:43 -0400 |
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| -1:000000000000 | 0:7564f3b1e675 |
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| 1 # ----------------------------------------------------------------------# | |
| 2 # Copyright (c) 2011, Richard Lupat & Jason Li. | |
| 3 # | |
| 4 # > Source License < | |
| 5 # This file is part of CONTRA. | |
| 6 # | |
| 7 # CONTRA is free software: you can redistribute it and/or modify | |
| 8 # it under the terms of the GNU General Public License as published by | |
| 9 # the Free Software Foundation, either version 3 of the License, or | |
| 10 # (at your option) any later version. | |
| 11 # | |
| 12 # CONTRA is distributed in the hope that it will be useful, | |
| 13 # but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| 15 # GNU General Public License for more details. | |
| 16 # | |
| 17 # You should have received a copy of the GNU General Public License | |
| 18 # along with CONTRA. If not, see <http://www.gnu.org/licenses/>. | |
| 19 # | |
| 20 # | |
| 21 #-----------------------------------------------------------------------# | |
| 22 # Last Updated : 28 Mar 2011 11:00AM | |
| 23 | |
| 24 class Target: | |
| 25 """ | |
| 26 Class for target regions | |
| 27 """ | |
| 28 | |
| 29 population = 0 | |
| 30 | |
| 31 def __init__(self): | |
| 32 self.id = 0 | |
| 33 self.gene = "unknown" | |
| 34 self.chr = "chr1" | |
| 35 self.start = 0 | |
| 36 self.end = 0 | |
| 37 self.numberExon = 0 | |
| 38 self.oriStart = 0 | |
| 39 self.oriEnd = 0 | |
| 40 | |
| 41 def convertTarget(target): | |
| 42 targets = open(target) | |
| 43 | |
| 44 targetList = [] | |
| 45 | |
| 46 count = 0 | |
| 47 for region in targets: | |
| 48 region = region.split() | |
| 49 chr = "chr" + region[0].strip("chr") | |
| 50 start = region[1] | |
| 51 end = region[2] | |
| 52 try: | |
| 53 gene = region[3] | |
| 54 except: | |
| 55 gene = "unknown" | |
| 56 count += 1 | |
| 57 | |
| 58 aTarget = Target() | |
| 59 aTarget.id = count | |
| 60 aTarget.gene = gene | |
| 61 aTarget.chr = chr | |
| 62 aTarget.start = start | |
| 63 aTarget.end = end | |
| 64 aTarget.numberExon = 1 | |
| 65 aTarget.oriStart = start | |
| 66 aTarget.oriEnd = end | |
| 67 | |
| 68 targetList.append(aTarget) | |
| 69 | |
| 70 | |
| 71 return targetList |