Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/CoordsParser.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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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.Mapping import Mapping |
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33 from commons.core.parsing.MapperParser import MapperParser |
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34 from SMART.Java.Python.structure.SubMapping import SubMapping |
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35 from SMART.Java.Python.misc import Utils |
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36 |
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37 class CoordsParser(MapperParser): |
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38 """A class that parses the .coords output of Nucmer""" |
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39 |
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40 def __init__(self, fileName, verbosity = 0): |
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41 self._lineParseRe = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+\|\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+\|\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+\|\s+(?P<identity>\d+\.?\d*)\s+\|\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$") |
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42 self._lineParseRe2 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+(?P<identity>\d+\.?\d*)\s+(?P<rlen>\d+\.?\d*)\s+(?P<qlen>\d+\.?\d*)\s+(?P<rcov>\d+\.?\d*)\s+(?P<qcov>\d+\.?\d*)\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$") |
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43 self._lineParseRe3 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+\|\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+\|\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+\|\s+(?P<identity>\d+\.?\d*)\s+(?P<sim>\d+\.?\d*)\s+(?P<stp>\d+\.?\d*)\s+\|\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$") |
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44 self._lineParseRe4 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+(?P<identity>\d+\.?\d*)\s+(?P<sim>\d+\.?\d*)\s+(?P<stp>\d+\.?\d*)\s+(?P<rlen>\d+\.?\d*)\s+(?P<qlen>\d+\.?\d*)\s+(?P<rcov>\d+\.?\d*)\s+(?P<qcov>\d+\.?\d*)\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$") |
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45 self.lineType = 1 |
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46 MapperParser.__init__(self, fileName, verbosity) |
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47 |
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48 def getFileFormats(): |
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49 return ["coords"] |
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50 getFileFormats = staticmethod(getFileFormats) |
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51 |
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52 def skipFirstLines(self): |
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53 while True: |
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54 line = self.handle.readline() |
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55 self.currentLineNb += 1 |
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56 if line == "": |
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57 break |
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58 if "=====" in line: |
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59 break |
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60 if "[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]" in line: |
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61 self.lineType = 2 |
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62 break |
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63 if "[S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] [% SIM] [% STP] | [FRM] [TAGS]" in line: |
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64 self.lineType = 3 |
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65 |
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66 if "[% IDY]\t[% SIM]\t[% STP]" in line and "[LEN Q]"in line: |
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67 self.lineType = 4 |
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68 break |
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69 |
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70 def parseLine(self, line): |
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71 |
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72 if self.lineType == 1 : |
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73 m = self._lineParseRe.search(line) |
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74 elif self.lineType == 2: |
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75 m = self._lineParseRe2.search(line) |
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76 elif self.lineType == 3: |
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77 m = self._lineParseRe3.search(line) |
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78 elif self.lineType == 4: |
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79 m = self._lineParseRe4.search(line) |
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80 if m == None: |
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81 sys.exit("\nLine %d '%s' does not have a NucMer format" % (self.currentLineNb, line)) |
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82 |
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83 mapping = Mapping() |
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84 |
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85 subMapping = SubMapping() |
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86 subMapping.queryInterval.setName(m.group("qName")) |
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87 subMapping.queryInterval.setStart(min(int(m.group("qStart")), int(m.group("qEnd")))) |
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88 subMapping.queryInterval.setEnd(max(int(m.group("qStart")), int(m.group("qEnd")))) |
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89 subMapping.queryInterval.setSize(int(m.group("qLength"))) |
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90 subMapping.queryInterval.setDirection(int(m.group("qEnd")) - int(m.group("qStart"))) |
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91 |
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92 subMapping.targetInterval.setChromosome(m.group("tName")) |
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93 subMapping.targetInterval.setStart(min(int(m.group("tStart")), int(m.group("tEnd")))) |
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94 subMapping.targetInterval.setEnd(max(int(m.group("tStart")), int(m.group("tEnd")))) |
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95 subMapping.targetInterval.setSize(int(m.group("tLength"))) |
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96 subMapping.targetInterval.setDirection(int(m.group("tEnd")) - int(m.group("tStart"))) |
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97 |
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98 subMapping.setDirection(int(m.group("qEnd")) - int(m.group("qStart"))) |
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99 subMapping.setSize(min(int(m.group("qLength")), int(m.group("tLength")))) |
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100 subMapping.setIdentity(float(m.group("identity"))) |
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101 |
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102 mapping.addSubMapping(subMapping) |
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103 mapping.targetInterval.setStart(min(int(m.group("tStart")), int(m.group("tEnd")))) |
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104 mapping.targetInterval.setEnd(max(int(m.group("tStart")), int(m.group("tEnd")))) |
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105 mapping.targetInterval.setSize(int(m.group("tLength"))) |
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106 mapping.targetInterval.setChromosome(m.group("tName")) |
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107 |
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108 mapping.queryInterval.setStart(min(int(m.group("qStart")), int(m.group("qEnd")))) |
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109 mapping.queryInterval.setEnd(max(int(m.group("qStart")), int(m.group("qEnd")))) |
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110 mapping.queryInterval.setSize(int(m.group("qLength"))) |
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111 mapping.queryInterval.setName(m.group("qName")) |
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112 mapping.setDirection(int(m.group("qEnd")) - int(m.group("qStart"))) |
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113 mapping.setSize(min(int(m.group("qLength")), int(m.group("tLength")))) |
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114 mapping.setIdentity(float(m.group("identity"))) |
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115 mapping.setTagValue("feature", "match") |
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116 mapping.setTagValue("Target", "%s %d %d" % (m.group("qName"), int(m.group("qStart")), int(m.group("qEnd")))) |
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117 |
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118 if self.lineType ==2 or self.lineType ==4: |
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119 mapping.setTagValue("target_pident", float(m.group("identity"))) |
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120 mapping.setTagValue("target_pcover", float(m.group("qcov"))) |
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121 mapping.setTagValue("target_length", int(m.group("qlen"))) |
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122 |
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123 |
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124 # Specific to Mark Work. Commented lines because of possible slowdown. |
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125 # for line in self.handle: |
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126 # string1 = line.strip() |
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127 # self.currentLineNb += 1 |
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128 # break |
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129 # for line in self.handle: |
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130 # string2 = line.strip() |
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131 # self.currentLineNb += 1 |
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132 # break |
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133 # print(len(string1),len(string2)) |
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134 # mapping.setNbMismatches(Utils.getHammingDistance(string1, string2)) |
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135 mapping.setNbGaps(0) |
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136 |
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137 return mapping |