1 | package nl.tno.massSequencing |
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2 | |
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3 | import org.codehaus.groovy.grails.commons.ConfigurationHolder |
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4 | |
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5 | class SequenceData { |
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6 | def fileService |
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7 | |
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8 | String sequenceFile = '' |
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9 | String qualityFile = '' |
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10 | Long numSequences = 0L |
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11 | Float averageQuality = 0.0 |
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12 | |
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13 | static belongsTo = [sample: AssaySample] |
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14 | static constraints = { |
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15 | qualityFile(nullable: true) |
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16 | numSequences(nullable: true) |
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17 | averageQuality(nullable: true) |
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18 | } |
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19 | |
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20 | /** |
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21 | * Returns the number of files in this data object. |
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22 | * @return |
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23 | */ |
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24 | public int numFiles() { |
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25 | int number = 0; |
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26 | if( sequenceFile != null && sequenceFile != "" ) |
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27 | number++; |
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28 | |
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29 | if( qualityFile != null && qualityFile != "" ) |
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30 | number++; |
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31 | |
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32 | return number; |
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33 | } |
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34 | |
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35 | |
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36 | /** |
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37 | * Returns the number of quality scores in this data object. This equals |
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38 | * the number of sequences iff a quality score is attached to this object |
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39 | * |
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40 | * @return Number of quality scores in this object |
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41 | */ |
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42 | public int numQualScores() { |
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43 | if( qualityFile != null ) |
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44 | return numSequences |
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45 | else |
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46 | return 0; |
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47 | } |
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48 | |
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49 | def beforeDelete = { |
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50 | def permanentDir = fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir.toString() ) |
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51 | if( sequenceFile ) { |
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52 | fileService.delete( sequenceFile, permanentDir ) |
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53 | } |
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54 | |
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55 | if( qualityFile ) |
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56 | fileService.delete( qualityFile, permanentDir ) |
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57 | |
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58 | // Reset statistics of the assay sample, to ensure the deleted files are removed from statistics |
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59 | sample?.resetStats(); |
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60 | |
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61 | return true; |
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62 | } |
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63 | |
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64 | public SequenceData clone() { |
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65 | // Copy the files to a new name |
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66 | def permanentDir = fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir.toString() ) |
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67 | |
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68 | def newSequenceFileName = sequenceFile; |
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69 | if( this.sequenceFile ) { |
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70 | newSequenceFileName = fileService.getUniqueFilename( this.sequenceFile, permanentDir ); |
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71 | fileService.copy( sequenceFile, newSequenceFileName, permanentDir ); |
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72 | } |
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73 | |
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74 | def newQualityFileName = qualityFile; |
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75 | if( this.qualityFile ) { |
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76 | newQualityFileName = fileService.getUniqueFilename( this.qualityFile, permanentDir ); |
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77 | fileService.copy( qualityFile, newQualityFileName, permanentDir ); |
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78 | } |
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79 | |
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80 | def sd = new SequenceData( |
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81 | sequenceFile: newSequenceFileName, |
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82 | qualityFile: newQualityFileName, |
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83 | numSequences: this.numSequences, |
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84 | averageQuality: this.averageQuality |
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85 | ); |
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86 | |
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87 | if( this.sample ) |
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88 | this.sample.addToSequenceData( sd ); |
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89 | |
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90 | return sd; |
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91 | } |
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92 | } |
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