Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/GbParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # Copyright INRA-URGI 2009-2010 |
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3 # |
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4 # This software is governed by the CeCILL license under French law and |
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5 # abiding by the rules of distribution of free software. You can use, |
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6 # modify and/ or redistribute the software under the terms of the CeCILL |
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7 # license as circulated by CEA, CNRS and INRIA at the following URL |
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8 # "http://www.cecill.info". |
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9 # |
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10 # As a counterpart to the access to the source code and rights to copy, |
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11 # modify and redistribute granted by the license, users are provided only |
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12 # with a limited warranty and the software's author, the holder of the |
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13 # economic rights, and the successive licensors have only limited |
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14 # liability. |
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15 # |
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16 # In this respect, the user's attention is drawn to the risks associated |
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17 # with loading, using, modifying and/or developing or reproducing the |
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18 # software by the user in light of its specific status of free software, |
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19 # that may mean that it is complicated to manipulate, and that also |
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20 # therefore means that it is reserved for developers and experienced |
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21 # professionals having in-depth computer knowledge. Users are therefore |
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22 # encouraged to load and test the software's suitability as regards their |
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23 # requirements in conditions enabling the security of their systems and/or |
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24 # data to be ensured and, more generally, to use and operate it in the |
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25 # same conditions as regards security. |
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26 # |
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27 # The fact that you are presently reading this means that you have had |
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28 # knowledge of the CeCILL license and that you accept its terms. |
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29 # |
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30 import re |
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31 import sys |
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32 from SMART.Java.Python.structure.Interval import Interval |
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33 from SMART.Java.Python.structure.Transcript import Transcript |
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34 from commons.core.parsing.TranscriptListParser import TranscriptListParser |
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35 |
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36 |
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37 class GbParser(TranscriptListParser): |
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38 """A class that parses a GBrowse file and create a transcript list""" |
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39 |
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40 |
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41 def __init__(self, fileName, verbosity = 0): |
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42 self.reference = None |
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43 self.color = None |
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44 super(GbParser, self).__init__(fileName, verbosity) |
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45 |
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46 |
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47 def __del__(self): |
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48 super(GbParser, self).__del__() |
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49 |
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50 |
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51 def getFileFormats(): |
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52 return ["gb", "gbrowse"] |
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53 getFileFormats = staticmethod(getFileFormats) |
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54 |
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55 |
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56 def skipFirstLines(self): |
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57 for line in self.handle: |
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58 self.currentLineNb += 1 |
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59 line = line.strip() |
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60 m = re.search(r"^\s*bgcolor\s*=\s*(\S+)\s*$", line) |
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61 if m != None: |
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62 self.color = m.group(1) |
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63 if line == "": |
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64 return |
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65 |
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66 |
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67 def parseLine(self, line): |
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68 transcript = Transcript() |
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69 # first line (reference) |
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70 m = re.search(r"^\s*reference\s*=\s*(\S+)\s*$", line) |
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71 if m != None: |
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72 self.reference = m.group(1) |
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73 for line in self.handle: |
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74 line = line.strip() |
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75 self.currentLineNb += 1 |
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76 break |
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77 # second line (genomic coordinates) |
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78 m = re.search(r"^\s*READS\s+(\S+)\s+(\S+)\s+\"([^\"]*)\"\s*$", line) |
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79 if m == None: |
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80 sys.exit("\nLine %d '%s' does not have a GBrowse format" % (self.currentLineNb, line)) |
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81 if self.reference == None: |
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82 sys.exit("Cannot get reference of GBrowse line %d '%s'" % (self.currentLineNb, line)) |
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83 transcript.setChromosome(self.reference) |
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84 transcript.setName(m.group(1)) |
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85 transcript.setComment(m.group(3)) |
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86 # exons |
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87 exons = m.group(2).split(",") |
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88 transcriptStart = 1000000000 |
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89 transcriptEnd = 0 |
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90 direction = 0 |
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91 for exon in exons: |
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92 m = re.search(r"^(\d+)-(\d+)$", exon) |
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93 if m == None: |
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94 sys.exit("\nCannot read GBrowse exon line %d '%s'" % (self.currentLineNb, exon)) |
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95 interval = Interval() |
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96 interval.setChromosome(transcript.chromosome) |
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97 direction += int(m.group(2)) - int(m.group(1)) |
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98 start = min(int(m.group(1)), int(m.group(2))) |
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99 end = max(int(m.group(1)), int(m.group(2))) |
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100 interval.setStart(start) |
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101 interval.setEnd(end) |
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102 transcriptStart = min(transcriptStart, start) |
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103 transcriptEnd = max(transcriptEnd, end) |
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104 transcript.addExon(interval) |
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105 transcript.setStart(transcriptStart) |
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106 transcript.setEnd(transcriptEnd) |
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107 transcript.setDirection(direction) |
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108 for exon in transcript.getExons(): |
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109 exon.setDirection(direction) |
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110 return transcript |
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111 |