Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/ElandParser.py @ 4:1fc014126d55
Uploaded
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:45:50 -0500 |
parents | e0f8dcca02ed |
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rev | line source |
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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 sys |
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31 from commons.core.parsing.MapperParser import MapperParser |
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32 from SMART.Java.Python.structure import Mapping |
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33 |
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34 class ElandParser(MapperParser): |
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35 """A class that parses ELAND format""" |
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36 |
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37 def __init__(self, fileName, verbosity = 0): |
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38 super(ElandParser, self).__init__(fileName, verbosity) |
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39 |
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40 |
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41 def __del__(self): |
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42 super(ElandParser, self).__del__() |
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43 |
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44 |
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45 def getFileFormats(): |
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46 return ["eland"] |
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47 getFileFormats = staticmethod(getFileFormats) |
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48 |
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49 |
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50 def skipFirstLines(self): |
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51 pass |
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52 |
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53 |
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54 def getInfos(self): |
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55 super(ElandParser, self).getInfos() |
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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 line = line.strip() |
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61 |
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62 fields = line.split("\t") |
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63 if len(fields) < 22: |
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64 sys.exit("Line %d '%s' does not look like a ELAND line (number of fields is %d instead of 22)" % (self.currentLineNb, line, len(fields))) |
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65 |
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66 flowCell = fields[0] |
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67 run = fields[1] |
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68 lane = fields[2] |
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69 tile = fields[3] |
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70 xcoord = fields[4] |
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71 ycoord = fields[5] |
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72 index = fields[6] |
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73 number = fields[7] |
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74 read = fields[8] |
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75 quality = fields[9] |
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76 chromosome = fields[10] |
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77 contig = fields[11] |
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78 position = fields[12] |
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79 strand = fields[13] |
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80 description = fields[14] |
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81 singleScore = fields[15] |
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82 pairScore = fields[16] |
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83 partnerChromosome = fields[17] |
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84 partnerContig = fields[18] |
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85 partnerOffset = fields[19] |
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86 partnerStrand = fields[20] |
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87 filtering = fields[21] |
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88 |
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89 if number != "1": |
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90 sys.exit("S-MART cannot handle pair-end reads yet!") |
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91 |
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92 # nothing found |
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93 if position == "": |
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94 return None |
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95 |
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96 name = "%s_%s:%s:%s:%s:%s#0/1" % (flowCell, run, lane, tile, xcoord, ycoord) |
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97 direction = 1 if strand == "F" else -1 |
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98 nbMismatches = 0 |
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99 for char in description: |
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100 if ord("A") <= ord(char) and ord(char) <= ord("Z"): |
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101 nbMismatches += 1 |
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102 |
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103 mapping = Mapping() |
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104 mapping.setTagValue("qualityString", quality) |
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105 |
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106 mapping.queryInterval.setName(name) |
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107 mapping.queryInterval.setDirection(direction) |
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108 mapping.queryInterval.setStart(1) |
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109 mapping.queryInterval.setEnd(len(read)) |
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110 |
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111 mapping.targetInterval.setChromosome(chromosome) |
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112 mapping.targetInterval.setStart(int(position)) |
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113 mapping.targetInterval.setEnd(int(position) + len(read)) |
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114 mapping.targetInterval.setDirection(1) |
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115 |
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116 mapping.setSize(len(read)) |
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117 mapping.setDirection(direction) |
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118 |
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119 mapping.setNbGaps(0) |
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120 mapping.setNbMismatches(nbMismatches) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
diff
changeset
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121 mapping.setTagValue("score", int(singleScore)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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122 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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123 if filtering == "Y": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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124 return mapping |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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125 # mapping filtered out |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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126 return None |