Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/ExoParser.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 commons.core.parsing.MapperParser import MapperParser |
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33 from SMART.Java.Python.structure.Mapping import Mapping |
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34 from SMART.Java.Python.structure.SubMapping import SubMapping |
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35 |
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36 class ExoParser(MapperParser): |
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37 """A class that parses the output of Exonerate - roll your own format""" |
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38 |
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39 def __init__(self, fileName, verbosity = 0): |
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40 super(ExoParser, self).__init__(fileName, verbosity) |
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41 |
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42 |
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43 def __del__(self): |
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44 super(ExoParser, self).__del__() |
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45 |
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46 |
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47 def getFileFormats(): |
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48 return ["exo", "exonerate"] |
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49 getFileFormats = staticmethod(getFileFormats) |
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50 |
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51 |
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52 def skipFirstLines(self): |
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53 while "Hostname" not in self.handle.readline(): |
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54 self.currentLineNb += 1 |
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55 pass |
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56 |
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57 |
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58 def parseLine(self, line): |
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59 |
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60 if line == "-- completed exonerate analysis\n": |
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61 return None |
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62 |
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63 m = re.search(r"^\s*(\S+)\s+(\d+)\s+(\d+)\s+[+-]\s+(\S+)\s+(\d+)\s+(\d+)\s+([+-])\s+\d+\s+(\d+)\s+(\S.*)$", line) |
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64 if m == None: |
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65 sys.exit("\nLine %d '%s' does not have a RYO format" % (self.currentLineNb, line)) |
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66 |
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67 mapping = Mapping() |
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68 name = m.group(1) |
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69 queryStart = min(int(m.group(2)), int(m.group(3))) |
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70 queryEnd = max(int(m.group(2)), int(m.group(3)))-1 |
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71 chromosome = m.group(4) |
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72 targetStart = min(int(m.group(5)), int(m.group(6))) |
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73 targetEnd = max(int(m.group(5)), int(m.group(6)))-1 |
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74 direction = m.group(7) |
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75 nbMismatches = int(m.group(8)) |
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76 rest = m.group(9).strip() |
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77 |
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78 nbGaps = 0 |
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79 queryOffset = 0 |
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80 targetOffset = 0 |
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81 |
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82 subMapping = None |
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83 m = re.search(r"^(\w)\s+(\d+)\s+(\d+)", rest) |
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84 while m != None: |
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85 queryDistance = int(m.group(2)) |
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86 targetDistance = int(m.group(3)) |
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87 if m.group(1) == "M": |
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88 if subMapping == None: |
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89 subMapping = SubMapping() |
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90 |
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91 subMapping.setSize(queryDistance) |
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92 subMapping.setDirection(direction) |
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93 |
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94 subMapping.queryInterval.setName(name) |
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95 subMapping.queryInterval.setStart(queryStart + queryOffset) |
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96 subMapping.queryInterval.setDirection(direction) |
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97 |
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98 subMapping.targetInterval.setChromosome(chromosome) |
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99 subMapping.targetInterval.setStart(targetStart + targetOffset) |
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100 subMapping.targetInterval.setDirection(1) |
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101 |
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102 elif m.group(1) == "G": |
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103 nbGaps += max(queryDistance, targetDistance) |
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104 |
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105 elif m.group(1) == "I" or m.group(1) == "5" or m.group(1) == "3": |
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106 if subMapping != None: |
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107 subMapping.queryInterval.setEnd(queryStart + queryOffset - 1) |
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108 subMapping.targetInterval.setEnd(targetStart + targetOffset - 1) |
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109 mapping.addSubMapping(subMapping) |
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110 subMapping = None |
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111 else: |
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112 sys.exit("Cannot understand sign '%s' in line %s" % (m.group(1), line)) |
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113 |
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114 queryOffset += queryDistance |
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115 targetOffset += targetDistance |
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116 rest = rest[m.end():].strip() |
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117 m = re.search(r"^(\w)\s+(\d+)\s+(\d+)", rest) |
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118 |
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119 if subMapping != None: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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120 subMapping.queryInterval.setEnd(queryStart + queryOffset - 1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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121 subMapping.targetInterval.setEnd(targetStart + targetOffset - 1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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122 mapping.addSubMapping(subMapping) |
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123 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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124 mapping.setNbMismatches(nbMismatches) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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125 mapping.setNbGaps(nbGaps) |
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126 mapping.setDirection(direction) |
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127 |
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128 mapping.queryInterval.setName(name) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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129 mapping.queryInterval.setStart(queryStart) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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130 mapping.queryInterval.setEnd(queryEnd) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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131 |
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132 mapping.targetInterval.setChromosome(chromosome) |
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133 mapping.targetInterval.setStart(targetStart) |
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134 mapping.targetInterval.setEnd(targetEnd) |
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135 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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136 return mapping |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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137 |