changeset 31:0ab839023fe4

Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 5677346472b5
children 3441fe98a2ba
files SMART/DiffExpAnal/DESeqTools/HTseqClean.R SMART/DiffExpAnal/DESeqTools/MAplotDE.R SMART/DiffExpAnal/DESeqTools/RNAseqFunctions.R SMART/DiffExpAnal/DESeqTools/anadiffGenes2conds.R SMART/DiffExpAnal/DESeqTools/barplotNul.R SMART/DiffExpAnal/DESeqTools/barplotTC.R SMART/DiffExpAnal/DESeqTools/boxplotCounts.R SMART/DiffExpAnal/DESeqTools/clusterPlot.R SMART/DiffExpAnal/DESeqTools/densityPlot.R SMART/DiffExpAnal/DESeqTools/exportComplete.R SMART/DiffExpAnal/DESeqTools/exportDiff.R SMART/DiffExpAnal/DESeqTools/histoRawp.R SMART/DiffExpAnal/DESeqTools/loadCountData.R SMART/DiffExpAnal/DESeqTools/loadTargetFile.R SMART/DiffExpAnal/DESeqTools/majSequence.R SMART/DiffExpAnal/DESeqTools/pairwiseSERE.R SMART/DiffExpAnal/DESeqTools/pairwiseScatterPlots.R SMART/DiffExpAnal/DESeqTools/plotDispEstimates.R SMART/DiffExpAnal/DESeqTools/raw/f1cond1.tsv SMART/DiffExpAnal/DESeqTools/raw/f1cond2.tsv SMART/DiffExpAnal/DESeqTools/raw/f2cond1.tsv SMART/DiffExpAnal/DESeqTools/raw/f2cond2.tsv SMART/DiffExpAnal/DESeqTools/raw2counts.R SMART/DiffExpAnal/DESeqTools/removeNul.R SMART/DiffExpAnal/__init__.py SMART/DiffExpAnal/bam_to_sam_parallel.py SMART/DiffExpAnal/bam_to_sam_parallel.xml SMART/DiffExpAnal/bam_to_sam_parallel_unSQL.py SMART/DiffExpAnal/bam_to_sam_parallel_unSQL.xml SMART/DiffExpAnal/compareOverlapping_parallel.py SMART/DiffExpAnal/compareOverlapping_parallel.xml SMART/DiffExpAnal/compareOverlapping_parallel_unSQL.py SMART/DiffExpAnal/compareOverlapping_parallel_unSQL.xml SMART/DiffExpAnal/countNumber.pl SMART/DiffExpAnal/countNumber.xml SMART/DiffExpAnal/countNumber_parallel.py SMART/DiffExpAnal/countNumber_parallel.xml SMART/DiffExpAnal/countNumber_parallel_unSQL.py SMART/DiffExpAnal/countNumber_parallel_unSQL.xml SMART/DiffExpAnal/deseq.sh SMART/DiffExpAnal/deseq.xml SMART/DiffExpAnal/fastq_groomer_parallel.py SMART/DiffExpAnal/fastq_groomer_parallel.xml SMART/DiffExpAnal/fastq_groomer_parallel_unSQL.py SMART/DiffExpAnal/fastq_groomer_parallel_unSQL.xml SMART/DiffExpAnal/gsnap.xml SMART/DiffExpAnal/gsnap_parallel_unSQL.py SMART/DiffExpAnal/gsnap_parallel_unSQL.xml SMART/DiffExpAnal/listInputs.pl SMART/DiffExpAnal/listInputs.xml SMART/DiffExpAnal/loadHTSeqResultFiles.py SMART/DiffExpAnal/loadHTSeqResultFiles.xml SMART/DiffExpAnal/loadMultiFastqFiles.py SMART/DiffExpAnal/loadMultiFastqFiles.sh SMART/DiffExpAnal/loadMultiFastqFiles.xml SMART/DiffExpAnal/testR.R SMART/DiffExpAnal/testR.sh SMART/DiffExpAnal/tophat_parallel.py SMART/DiffExpAnal/tophat_parallel.xml SMART/DiffExpAnal/tophat_parallel_unSQL.py SMART/DiffExpAnal/tophat_parallel_unSQL.xml SMART/DiffExpAnal/wrappGSNAP.py SMART/Java/File.java SMART/Java/Files.java SMART/Java/FormatType.java SMART/Java/FormatsContainer.java SMART/Java/FormatsReader.java SMART/Java/Global.java SMART/Java/Installer/Old/PasswordAsker.java SMART/Java/Installer/Old/SmartInstaller.java SMART/Java/Installer/Old/SmartInstallerTask.java SMART/Java/Installer/PasswordAsker.java SMART/Java/Installer/SmartInstaller.jar SMART/Java/Installer/SmartInstaller.java SMART/Java/Installer/SmartInstallerTask.java SMART/Java/Installer/build.sh SMART/Java/Installer/manifest.txt SMART/Java/Installer/s-mart.zip SMART/Java/Program.java SMART/Java/ProgramFileReader.java SMART/Java/ProgramLauncher.java SMART/Java/ProgramOption.java SMART/Java/Python/.RData SMART/Java/Python/.gitignore SMART/Java/Python/100% SMART/Java/Python/CompareOverlapping.pyc SMART/Java/Python/CountLoci.py SMART/Java/Python/GetFlanking.pyc SMART/Java/Python/GetIntersection.py SMART/Java/Python/GetUpDownStream.pyc SMART/Java/Python/Helitrons.fasta SMART/Java/Python/Rplots.pdf SMART/Java/Python/S1_S3_blast.blast SMART/Java/Python/TestFiles/SR1.fastq SMART/Java/Python/TestFiles/Wig/chr1.wig SMART/Java/Python/TestFiles/adress.txt SMART/Java/Python/TestFiles/clusterize_default_expected.gff3 SMART/Java/Python/TestFiles/clusterize_default_expected.map SMART/Java/Python/TestFiles/clusterize_normalize_expected.gff3 SMART/Java/Python/TestFiles/clusterize_output_tag_expected.gff3 SMART/Java/Python/TestFiles/clusterize_strands_expected.gff3 SMART/Java/Python/TestFiles/expOutputGff.gff3 SMART/Java/Python/TestFiles/expRef.fasta SMART/Java/Python/TestFiles/inputCR.gff3 SMART/Java/Python/TestFiles/inputFileTest1.bed SMART/Java/Python/TestFiles/inputFileTest2.bed SMART/Java/Python/TestFiles/inputMSWC1.gff3 SMART/Java/Python/TestFiles/inputMSWC2.gff3 SMART/Java/Python/TestFiles/inputMTC.sam SMART/Java/Python/TestFiles/inputMapping.map SMART/Java/Python/TestFiles/mapperAnalyzerExpected.gff3 SMART/Java/Python/TestFiles/mapperAnalyzerMappings.axt SMART/Java/Python/TestFiles/mapperAnalyzerOutput.gff3 SMART/Java/Python/TestFiles/mapperAnalyzerSequences.mfq SMART/Java/Python/TestFiles/sorted_file_oneline.gff3 SMART/Java/Python/TestFiles/sorted_query.gff3 SMART/Java/Python/TestFiles/sorted_query_wig.wig SMART/Java/Python/TestFiles/sorted_ref.gff3 SMART/Java/Python/TestFiles/testBedParser1.bed SMART/Java/Python/TestFiles/testC2S.fa SMART/Java/Python/TestFiles/testC2S.gff3 SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceAntisense1.gff3 SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceAntisense2.gff3 SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceSimple1.gff3 SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceSimple2.gff3 SMART/Java/Python/TestFiles/testDifferentialExpressionExpected.gff3 SMART/Java/Python/TestFiles/testDifferentialExpressionOutput.gff3 SMART/Java/Python/TestFiles/testDifferentialExpressionReference.gff3 SMART/Java/Python/TestFiles/testDifferentialExpressionSample1.gff3 SMART/Java/Python/TestFiles/testDifferentialExpressionSample2.gff3 SMART/Java/Python/TestFiles/testGffParser1.gff3 SMART/Java/Python/TestFiles/testPlot.gff3 SMART/Java/Python/TestFiles/testSW.gff3 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptList1.bed SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptList2.bed SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListGetDifference1.gff3 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListGetDifference2.gff3 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeAggregation1.bed SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeAggregation2.bed SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSenseAntiSenseAway1.bed SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSenseAntiSenseAway1_modif.bed SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSenseAntiSenseAway2.bed SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSimple1.bed SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSimple2.bed SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListSelfMerge1.gff3 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListSelfMergeDifferentClusters1.bed SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListSelfMergeSense1.bed SMART/Java/Python/TestFiles/testTranscriptNormalize.gff3 SMART/Java/Python/TestFiles/test_distance.bed SMART/Java/Python/TestFiles/test_minoverlapp.bed SMART/Java/Python/__init__.pyc SMART/Java/Python/cleanGff.pyc SMART/Java/Python/cleaning/CleanerChooser.pyc SMART/Java/Python/cleaning/DefaultCleaner.pyc SMART/Java/Python/cleaning/GffCleaner.pyc SMART/Java/Python/cleaning/GtfCleaner.pyc SMART/Java/Python/cleaning/TranscriptListCleaner.pyc SMART/Java/Python/cleaning/__init__.pyc SMART/Java/Python/compare_TAIR10_Reiterative4th.gff3 SMART/Java/Python/fo.py SMART/Java/Python/genes.gtf SMART/Java/Python/genome.fasta SMART/Java/Python/gf.py SMART/Java/Python/misc/MultipleRPlotter.pyc SMART/Java/Python/misc/Progress.pyc SMART/Java/Python/misc/RPlotter.py SMART/Java/Python/misc/RPlotter.pyc SMART/Java/Python/misc/UnlimitedProgress.pyc SMART/Java/Python/misc/Utils.pyc SMART/Java/Python/misc/__init__.pyc SMART/Java/Python/mySql/MySqlConnection.pyc SMART/Java/Python/mySql/MySqlExonTable.pyc SMART/Java/Python/mySql/MySqlQuery.pyc SMART/Java/Python/mySql/MySqlTable.pyc SMART/Java/Python/mySql/MySqlTranscriptTable.pyc SMART/Java/Python/mySql/__init__.pyc SMART/Java/Python/ncList/.NCList.py.swp SMART/Java/Python/ncList/.NCListCursor.py.swp SMART/Java/Python/ncList/Benchmark.py SMART/Java/Python/ncList/ConvertToNCList.pyc SMART/Java/Python/ncList/FileSorter.pyc SMART/Java/Python/ncList/NCIndex.pyc SMART/Java/Python/ncList/NCList.pyc SMART/Java/Python/ncList/NCListCursor.pyc SMART/Java/Python/ncList/NCListFilePickle.pyc SMART/Java/Python/ncList/NCListHandler.pyc SMART/Java/Python/ncList/NCListMerger.pyc SMART/Java/Python/ncList/NCListParser.pyc SMART/Java/Python/ncList/__init__.pyc SMART/Java/Python/re_filter_ratio_5_NbReads_100_samples_all_norm_Window100overlap50.gff3 SMART/Java/Python/removeEmptySequences.py SMART/Java/Python/script.Rout SMART/Java/Python/structure/Bins.pyc SMART/Java/Python/structure/Interval.pyc SMART/Java/Python/structure/Mapping.pyc SMART/Java/Python/structure/Sequence.pyc SMART/Java/Python/structure/SequenceList.pyc SMART/Java/Python/structure/SubMapping.pyc SMART/Java/Python/structure/Transcript.pyc SMART/Java/Python/structure/TranscriptContainer.pyc SMART/Java/Python/structure/TranscriptList.pyc SMART/Java/Python/structure/__init__.pyc SMART/Java/Python/test.gff3 SMART/Java/Python/test.pdf SMART/Java/Python/test.png SMART/Java/Python/test/MockGetLetterDistribution.py SMART/Java/Python/test/Test_F_Clusterize.py SMART/Java/Python/test/Test_F_ClusterizeByTags.py SMART/Java/Python/test/Test_F_CollapseReads.py SMART/Java/Python/test/Test_F_CombineTags.py SMART/Java/Python/test/Test_F_FindOverlapsOptim.py SMART/Java/Python/test/Test_F_GetDifferentialExpression.py SMART/Java/Python/test/Test_F_GetFlanking.py SMART/Java/Python/test/Test_F_GetRandomSubset.py SMART/Java/Python/test/Test_F_GetSizes.py SMART/Java/Python/test/Test_F_RestrictFromCoverage.py SMART/Java/Python/test/Test_F_clusterizeBySlidingWindows.py SMART/Java/Python/test/Test_F_compareOverlapping.py SMART/Java/Python/test/Test_F_convertTranscriptFile.py SMART/Java/Python/test/Test_F_coordinatesToSequence.py SMART/Java/Python/test/Test_F_findTss.py SMART/Java/Python/test/Test_F_getExons.py SMART/Java/Python/test/Test_F_getLetterDistribution.py SMART/Java/Python/test/Test_F_getRandomRegions.py SMART/Java/Python/test/Test_F_getReadDistribution.py SMART/Java/Python/test/Test_F_getWigData.py SMART/Java/Python/test/Test_F_getWigDistance.py SMART/Java/Python/test/Test_F_getWigProfile.py SMART/Java/Python/test/Test_F_mapperAnalyzer.py SMART/Java/Python/test/Test_F_mappingToCoordinates.py SMART/Java/Python/test/Test_F_mergeSlidingWindowsClusters.py SMART/Java/Python/test/Test_F_mergeTranscriptLists.py SMART/Java/Python/test/Test_F_plot.py SMART/Java/Python/test/Test_F_plotCoverage.py SMART/Java/Python/test/Test_F_qualToFastq.py SMART/Java/Python/test/Test_F_restrictSequenceList.py SMART/Java/Python/test/Test_F_selectByTag.py SMART/Java/Python/test/Test_F_trimSequences.py SMART/Java/Python/test/Test_FindOverlapsOptim.py SMART/Java/Python/test/Test_FindOverlaps_optim.py SMART/Java/Python/test/__init__.py SMART/Java/Python/test/timeResults.R SMART/Java/Python/test3.gff3 SMART/Java/Python/test3.png SMART/Java/Python/test3.png_I.png SMART/Java/Python/testInstall.py SMART/Java/Python/testOut.gff3 SMART/Java/PythonHelperReader.java SMART/Java/PythonProgramFinder$1.class SMART/Java/PythonProgramFinder.java SMART/Java/README.txt SMART/Java/Sav/File.java SMART/Java/Sav/Files.java SMART/Java/Sav/FormatType.java SMART/Java/Sav/FormatsContainer.java SMART/Java/Sav/FormatsReader.java SMART/Java/Sav/Global.java SMART/Java/Sav/Program.java SMART/Java/Sav/ProgramFileReader.java SMART/Java/Sav/ProgramLauncher.java SMART/Java/Sav/ProgramOption.java SMART/Java/Sav/PythonHelperReader.java SMART/Java/Sav/PythonProgramFinder.java SMART/Java/Sav/Smart.java SMART/Java/Smart$1.class SMART/Java/Smart$2.class SMART/Java/Smart.jar SMART/Java/Smart.java SMART/Java/SmartInstaller.jar SMART/Java/WindowsRegistry.java SMART/Java/__init__.pyc SMART/Java/formats.txt SMART/Java/manifest.txt SMART/__init__.pyc SMART/bacteriaRegulatoryRegion_Detection/changeName.py SMART/bacteriaRegulatoryRegion_Detection/changeName.xml SMART/bacteriaRegulatoryRegion_Detection/colorGff.pl SMART/bacteriaRegulatoryRegion_Detection/colorGff.xml SMART/bacteriaRegulatoryRegion_Detection/coverageGff.pl SMART/bacteriaRegulatoryRegion_Detection/coverageGff.xml SMART/bacteriaRegulatoryRegion_Detection/interElementGff.pl SMART/bacteriaRegulatoryRegion_Detection/interElementGff.xml SMART/bacteriaRegulatoryRegion_Detection/listGff.sh SMART/bacteriaRegulatoryRegion_Detection/prepareAnnot.sh SMART/bacteriaRegulatoryRegion_Detection/prepareAnnot.xml SMART/bacteriaRegulatoryRegion_Detection/seedGff.pl SMART/bacteriaRegulatoryRegion_Detection/seedGff.xml SMART/bacteriaRegulatoryRegion_Detection/sortGff.pl SMART/bacteriaRegulatoryRegion_Detection/sortGff.xml SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.pl SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.xml SMART/bacteriaRegulatoryRegion_Detection/strictlyIncludeGff.pl SMART/bacteriaRegulatoryRegion_Detection/strictlyIncludeGff.xml SMART/bacteriaRegulatoryRegion_Detection/writeResToHTML.py SMART/bacteriaRegulatoryRegion_Detection/writeResToHTML.xml SMART/data/REF.fasta SMART/data/REF.fasta.fai SMART/data/SR1.fasta SMART/data/SR1.fastq SMART/data/SR2.fastq SMART/data/bamFile.bam SMART/data/dummy.fasta SMART/data/expRef.fasta SMART/data/expRef_withoutSplit.fasta SMART/data/output.png SMART/data/part0.bam SMART/data/part0.sam SMART/data/part1.bam SMART/data/part1.sam SMART/data/part2.bam SMART/data/part2.sam SMART/data/part3.bam SMART/data/part3.sam SMART/data/part4.bam SMART/data/part4.sam SMART/data/samFile.sam SMART/data/sortedBamFile.bam SMART/data/test.gff.gff3 SMART/data/test_clusterize.gff3 SMART/data/test_clusterize2.gff3 SMART/galaxy/CleanTranscriptFile.xml SMART/galaxy/Clusterize.xml SMART/galaxy/CollapseReads.xml SMART/galaxy/CompareOverlappingSmallQuery.xml SMART/galaxy/CompareOverlappingSmallRef.xml SMART/galaxy/ConvertTranscriptFile.xml SMART/galaxy/ConvertTranscriptFile_BedToCsv.xml SMART/galaxy/ConvertTranscriptFile_BedToGff2.xml SMART/galaxy/ConvertTranscriptFile_BedToGff3.xml SMART/galaxy/ConvertTranscriptFile_BedToSam.xml SMART/galaxy/ConvertTranscriptFile_BlastToCsv.xml SMART/galaxy/ConvertTranscriptFile_BlastToGff2.xml SMART/galaxy/ConvertTranscriptFile_BlastToGff3.xml SMART/galaxy/ConvertTranscriptFile_BlastToSam.xml SMART/galaxy/ConvertTranscriptFile_FastqToFasta.xml SMART/galaxy/ConvertTranscriptFile_Gff2ToCsv.xml SMART/galaxy/ConvertTranscriptFile_Gff2ToGff3.xml SMART/galaxy/ConvertTranscriptFile_Gff2ToSam.xml SMART/galaxy/ConvertTranscriptFile_Gff3ToCsv.xml SMART/galaxy/ConvertTranscriptFile_Gff3ToGff2.xml SMART/galaxy/ConvertTranscriptFile_Gff3ToSam.xml SMART/galaxy/ConvertTranscriptFile_Gff3ToWig.xml SMART/galaxy/ConvertTranscriptFile_SamToCsv.xml SMART/galaxy/ConvertTranscriptFile_SamToGff2.xml SMART/galaxy/ConvertTranscriptFile_SamToGff3.xml SMART/galaxy/CountReadGCPercent.xml SMART/galaxy/DiffExpAnal.xml SMART/galaxy/FindOverlaps_optim.xml SMART/galaxy/GetDifferentialExpression.xml SMART/galaxy/GetFlanking.xml SMART/galaxy/SelectByTag.xml SMART/galaxy/WrappGetLetterDistribution.xml SMART/galaxy/changeGffFeatures.xml SMART/galaxy/changeTagName.xml SMART/galaxy/cleanGff.xml SMART/galaxy/clusterize.xml SMART/galaxy/clusterizeBySlidingWindows.xml SMART/galaxy/compareOverlapping.xml SMART/galaxy/computeCoverage.xml SMART/galaxy/coordinatesToSequence.xml SMART/galaxy/findTss.xml SMART/galaxy/getDifference.xml SMART/galaxy/getDistance.xml SMART/galaxy/getDistribution.xml SMART/galaxy/getExons.xml SMART/galaxy/getIntrons.xml SMART/galaxy/getNb.xml SMART/galaxy/getReadDistribution.xml SMART/galaxy/getSequence.xml SMART/galaxy/getSizes.xml SMART/galaxy/getWigData.xml SMART/galaxy/getWigDistance.xml SMART/galaxy/getWigProfile.xml SMART/galaxy/mapperAnalyzer.xml SMART/galaxy/mappingToCoordinates.xml SMART/galaxy/mergeSlidingWindowsClusters.xml SMART/galaxy/mergeTranscriptLists.xml SMART/galaxy/modifyFasta.xml SMART/galaxy/modifyGenomicCoordinates.xml SMART/galaxy/modifySequenceList.xml SMART/galaxy/plot.xml SMART/galaxy/plotCoverage.xml SMART/galaxy/plotGenomeCoverage.xml SMART/galaxy/plotRepartition.xml SMART/galaxy/plotTranscriptList.xml SMART/galaxy/qualToFastq.xml SMART/galaxy/removeExonLines.xml SMART/galaxy/restrictFromSize.xml SMART/galaxy/restrictSequenceList.xml SMART/galaxy/restrictTranscriptList.xml SMART/galaxy/test/CollapseReads.xml SMART/galaxy/test/Test_F_WrappGetLetterDistribution.py SMART/galaxy/test/__init__.py SMART/galaxy/testArgum.xml SMART/galaxy/testR.xml SMART/galaxy/tool_conf.xml SMART/galaxy/tool_dependencies.xml SMART/galaxy/trimAdaptor.xml SMART/galaxy/trimSequences.xml commons/__init__.pyc commons/core/LoggerFactory.pyc commons/core/__init__.pyc commons/core/checker/AbstractChecker.py commons/core/checker/CheckerException.py commons/core/checker/CheckerUtils.py commons/core/checker/ConfigChecker.py commons/core/checker/ConfigException.py commons/core/checker/ConfigValue.py commons/core/checker/IChecker.py commons/core/checker/OldConfigChecker.py commons/core/checker/RepetException.py commons/core/checker/RepetException.pyc commons/core/checker/__init__.py commons/core/checker/__init__.pyc commons/core/checker/test/TestSuite_Checker.py commons/core/checker/test/Test_CheckerUtils.py commons/core/checker/test/Test_ConfigChecker.py commons/core/checker/test/Test_ConfigValue.py commons/core/checker/test/Test_F_ConfigChecker.py commons/core/checker/test/Test_OldConfigChecker.py commons/core/checker/test/__init__.py commons/core/coord/Align.pyc commons/core/coord/Map.pyc commons/core/coord/Range.pyc commons/core/coord/__init__.pyc commons/core/coord/test/TestSuite_coord.py commons/core/coord/test/Test_Align.py commons/core/coord/test/Test_AlignUtils.py commons/core/coord/test/Test_ConvCoord.py commons/core/coord/test/Test_F_ConvCoord.py commons/core/coord/test/Test_Map.py commons/core/coord/test/Test_MapUtils.py commons/core/coord/test/Test_Match.py commons/core/coord/test/Test_MatchUtils.py commons/core/coord/test/Test_MergedRange.py commons/core/coord/test/Test_Path.py commons/core/coord/test/Test_PathUtils.py commons/core/coord/test/Test_Range.py commons/core/coord/test/Test_Set.py commons/core/coord/test/Test_SetUtils.py commons/core/coord/test/Test_SlidingWindow.py commons/core/coord/test/__init__.py commons/core/launcher/JobScriptTemplate.py commons/core/launcher/JobScriptTemplateLight.py commons/core/launcher/JobScriptWithFilesCopyTemplate.py commons/core/launcher/Launcher.py commons/core/launcher/Launcher2.py commons/core/launcher/LauncherUtils.py commons/core/launcher/WriteScript.py commons/core/launcher/__init__.py commons/core/launcher/test/Test_Launcher.py commons/core/launcher/test/Test_Launcher2.py commons/core/launcher/test/Test_LauncherUtils.py commons/core/launcher/test/Test_WriteScript.py commons/core/launcher/test/__init__.py commons/core/launcher/test/expFiles/expJobScriptSQLiteWithFilesCopyTemplate.py commons/core/launcher/test/expFiles/expJobScriptTemplate.py commons/core/launcher/test/expFiles/expJobScriptTemplateLight.py commons/core/launcher/test/expFiles/expJobScriptTemplate_cmdWith2Lines.py commons/core/launcher/test/expFiles/expJobScriptWithFilesCopyTemplate.py commons/core/parsing/AxtParser.py commons/core/parsing/AxtParser.pyc commons/core/parsing/BamParser.pyc commons/core/parsing/BedParser.pyc commons/core/parsing/BlastParser.pyc commons/core/parsing/BowtieParser.pyc commons/core/parsing/CoordsParser.pyc commons/core/parsing/ElandParser.pyc commons/core/parsing/ExoParser.pyc commons/core/parsing/FastaParser.py commons/core/parsing/FastaParser.pyc commons/core/parsing/FastqParser.pyc commons/core/parsing/GffParser.pyc commons/core/parsing/GtfParser.pyc commons/core/parsing/MapParser.pyc commons/core/parsing/MapperParser.pyc commons/core/parsing/MaqParser.pyc commons/core/parsing/NCListParser.pyc commons/core/parsing/ParserChooser.pyc commons/core/parsing/PklParser.pyc commons/core/parsing/PslParser.pyc commons/core/parsing/RmapParser.pyc commons/core/parsing/SamParser.pyc commons/core/parsing/SeqmapParser.pyc commons/core/parsing/SequenceListParser.pyc commons/core/parsing/ShrimpParser.pyc commons/core/parsing/Soap2Parser.pyc 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commons/tools/dbShuffle.py commons/tools/dbSplit.py commons/tools/filterOutMatcher.py commons/tools/getCumulLengthFromTEannot.py commons/tools/pathnum2id.py commons/tools/refalign2fasta.py commons/tools/removeDescriptionInFastaHeaderProgramLauncher.py commons/tools/replaceGreaterThanSymbolInFastaHeaderProgramLauncher.py commons/tools/setnum2id.py commons/tools/srptBlasterMatcher.py commons/tools/srptCreateTable.py commons/tools/srptExportTable.py commons/tools/srptGameXmlMaker.py commons/tools/srptPhyML.py commons/tools/srptTableOverlap.py commons/tools/tabFileReader.py commons/tools/tests/MockFastaForReplaceGreaterThanSymbolInFastaHeader.py commons/tools/tests/Test_AlignTEOnGenomeAccordingToAnnotation.py commons/tools/tests/Test_CalcCoordCumulLength.py commons/tools/tests/Test_ChangeSequenceHeaders.py commons/tools/tests/Test_CorrelateTEageWithGCcontent.py commons/tools/tests/Test_F_AlignTEOnGenomeAccordingToAnnotation.py commons/tools/tests/Test_F_CheckMysqlConnect.py commons/tools/tests/Test_F_FilterAlign.py commons/tools/tests/Test_F_GFF3Maker.py commons/tools/tests/Test_F_GameXmlMaker.py commons/tools/tests/Test_F_GetMultiAlignAndPhylogenyPerTErefSeq.py commons/tools/tests/Test_F_GetSpecificTELibAccordingToAnnotation.py commons/tools/tests/Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py commons/tools/tests/Test_F_LaunchBlaster.py commons/tools/tests/Test_F_LaunchBlasterInParallel.py commons/tools/tests/Test_F_LaunchMatcherInParallel.py commons/tools/tests/Test_F_MergeMatchsFiles.py commons/tools/tests/Test_F_PostAnalyzeTELib.py commons/tools/tests/Test_F_ReplaceGreaterThanSymbolInFastaHeader.py commons/tools/tests/Test_F_RetrieveInitHeaders.py commons/tools/tests/Test_F_SplicerFromAnnotation.py commons/tools/tests/Test_F_TEclassifierPE.py commons/tools/tests/Test_GetMultAlignAndPhylogenyPerTErefSeq.py commons/tools/tests/Test_GetSpecificTELibAccordingToAnnotation.py commons/tools/tests/Test_OrientSequences.py commons/tools/tests/Test_RmvPairAlignInChunkOverlaps.py commons/tools/tests/Test_SpliceTEsFromGenome.py commons/tools/tests/Test_getCumulLengthFromTEannot.py commons/tools/tests/Test_pathnum2id.py commons/tools/tests/Test_refalign2fasta.py commons/tools/tests/Test_srptTableOverlap.py commons/tools/tests/__init__.py
diffstat 910 files changed, 548946 insertions(+), 1212 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/HTseqClean.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,19 @@
+# HTseqClean
+# remove extra counts out of genes
+# for HTseq output
+
+# input : rawCounts
+# output : cleaned rawCounts
+
+# created Feb 6th, 2012
+# Modified Feb 16th, 2012
+# Marie-Agnes Dillies
+
+
+HTseqClean <- function( rawCounts ){
+
+  row2remove <- c("alignment_not_unique", "ambiguous", "no_feature", "not_aligned", "too_low_aQual")
+  rawCounts <- rawCounts[!rawCounts$Id %in% row2remove,]
+  rawCounts[is.na(rawCounts)] <- 0
+  return(rawCounts)
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/MAplotDE.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,16 @@
+# MAplotDE
+# MAplot of DE genes
+
+# input : res, alpha,OUT_MAplotDEName 
+# output : MAplot (png)
+
+MAplotDE <- function( res, alpha, OUT_MAplotDEName, out = TRUE ){
+
+ 	if (out) png( file=OUT_MAplotDEName )
+  
+ 	plot( res$baseMean, res$log2FoldChange, pch=".", xlab="Mean expression", ylab="log2FC", main="",
+  		log="x", col=ifelse(res$padj < alpha, "red", "black") )
+	abline(h=0, col="red")
+
+  	if (out) dev.off()
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/RNAseqFunctions.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,38 @@
+# RNAseqFunctions
+# when sourced, sources all R functions associated with RNAseq data analysis
+
+RNAseqFunctions <- function( RfuncDir ){
+  
+  source(paste(RfuncDir, "loadTargetFile.R", sep=""))
+  source(paste(RfuncDir, "loadCountData.R", sep=""))
+# source(paste(RfuncDir, "loadStrandData.R", sep=""))
+  source(paste(RfuncDir, "HTseqClean.R", sep=""))
+  source(paste(RfuncDir, "raw2counts.R", sep=""))
+  source(paste(RfuncDir, "barplotTC.R", sep=""))
+  source(paste(RfuncDir, "barplotNul.R", sep=""))
+  source(paste(RfuncDir, "removeNul.R", sep=""))
+  source(paste(RfuncDir, "densityPlot.R", sep=""))
+  source(paste(RfuncDir, "boxplotCounts.R", sep=""))
+  source(paste(RfuncDir, "majSequence.R", sep=""))
+  source(paste(RfuncDir, "clusterPlot.R", sep=""))
+  source(paste(RfuncDir, "pairwiseSERE.R", sep=""))
+  source(paste(RfuncDir, "pairwiseScatterPlots.R", sep=""))
+#  source(paste(RfuncDir, "pairwiseScatterPlotsAll.R", sep=""))
+  source(paste(RfuncDir, "plotDispEstimates.R", sep=""))
+#  source(paste(RfuncDir, "deseqByCond.R", sep="")) 
+#  source(paste(RfuncDir, "edgeRByCond.R", sep=""))  
+#  source(paste(RfuncDir, "fisher.R", sep=""))
+  source(paste(RfuncDir, "histoRawp.R", sep=""))
+#  source(paste(RfuncDir, "histoRawpMconds.R", sep=""))
+  source(paste(RfuncDir, "MAplotDE.R", sep=""))
+#  source(paste(RfuncDir, "MAplotDEMconds.R", sep=""))
+  source(paste(RfuncDir, "exportComplete.R", sep=""))
+#  source(paste(RfuncDir, "exportCompleteEdgeR.R", sep=""))
+#  source(paste(RfuncDir, "exportCompleteFisher.R", sep=""))
+#  source(paste(RfuncDir, "exportCompleteMconds.R", sep=""))
+#  source(paste(RfuncDir, "exportCompleteByCond.R", sep=""))
+#  source(paste(RfuncDir, "exportCompletePaired.R", sep=""))
+  source(paste(RfuncDir, "exportDiff.R", sep=""))
+#  source(paste(RfuncDir, "synthese.R", sep=""))
+#  source(paste(RfuncDir, "exportDiffByCond.R", sep=""))
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/anadiffGenes2conds.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,191 @@
+# Analyse differentielle de donnees d expression par gene
+# avec DESeq
+# 2 conditions
+
+args <- commandArgs()
+#print(args[1])
+#print(args[2])
+#print(args[3])
+#print(args[4])
+#print(args[5])
+#print(args[6])
+#output file names
+#print(args[7]) # HTML file name
+#print(args[8]) # HTML file all images directory 
+#print(args[9]) # complete xls file name
+#print(args[10])# UP xls file name
+#print(args[11]) #Down xls file name
+#print(args[12]) #the executable scipt (for getting the path)
+
+library(R2HTML)
+library(R.utils)
+
+#run example: 
+projectName <- "DESeqAnalysis"
+analysisVersion <- "V1"    # fitType=local, sharingMode=fit-only, method=blind 
+rawDir <- "raw"
+targetFile <- args[4]
+header <- as.integer(args[5]) #si on a header ou pas, si on a, header=1, sinon header=0
+withOutReplicates <- as.integer(args[6])
+
+#get the directory to write the results
+tab <- splitByPattern(args[7], pattern="/")
+res_dir <- ""
+for (e in tab[1:length(tab)-1]) { res_dir <- paste(res_dir, e, sep="")}
+#get the html output file name
+OUT_HTMLname <- args[7]
+#get the images directory to write to
+OUT_imgDir <- args[8]
+#if the directory dosen't existe, we should create it first
+
+alpha <- 0.05
+adjMethod <- "BH"
+outfile <- T
+runningScriptTab <-  splitByPattern(args[12], pattern="/")
+RfuncDir <- ""
+for (r in runningScriptTab[1:length(runningScriptTab)-1]) { RfuncDir <- paste(RfuncDir, r, sep="")} #find the path of executable script  
+RfuncDir <- paste(RfuncDir, "DESeqTools/", sep="") #define the function files path
+# Dossier contenant les fonctions
+print(RfuncDir)
+source( paste(RfuncDir, "RNAseqFunctions.R", sep="/") )
+
+# Chargement des packages et des fonctions
+library(DESeq)
+RNAseqFunctions(RfuncDir)
+# Chargement du target file
+target <- loadTargetFile( targetFile, header )
+# Chargement des donnees, construction d'une table de comptages par gene
+#have changed
+rawCounts <- loadCountData( target, header )
+conds <- unique(target$group)
+cond1 <- as.character(conds[1])
+cond2 <- as.character(conds[!conds == conds[1]])
+rawCounts <- HTseqClean( rawCounts )
+
+# Transformation en matrice de comptages
+counts <- raw2counts( rawCounts )[[1]]
+
+# Nombre de reads par echantillon
+OUT_barplotTCName <- paste(OUT_imgDir, "barplotTC.png", sep="/")
+barplotTC( counts, target$group, OUT_barplotTCName, out=outfile )
+
+# Proportion comptages nuls
+OUT_barplotNulName <- paste(OUT_imgDir, "barplotNul.png", sep="/")
+barplotNul( counts, target$group, OUT_barplotNulName, out=outfile )
+
+# Suppression comptages nuls
+counts <- removeNul( counts )[[1]]
+
+# Density plot
+OUT_densityPlotName <- paste(OUT_imgDir, "densityPlot.png", sep="/")
+densityPlot( counts, target$group, OUT_densityPlotName, out=outfile )
+
+# Boxplot
+OUT_boxplotCountsName <- paste(OUT_imgDir, "boxplotCounts.png", sep="/")
+boxplotCounts( counts, target$group, type = c("raw", "norm"), OUT_boxplotCountsName, out=outfile )
+# Sequence majoritaire
+OUT_majSequenceName <- paste(OUT_imgDir, "majSequence.png", sep="/")
+majSequence( counts, target$group, OUT_majSequenceName, out=outfile )
+
+# ScatterPlot between two samples
+OUT_scatterPlot <- paste(OUT_imgDir, "scatterPlot.png", sep="/")
+pairwiseScatterPlots(counts, target, OUT_scatterPlot, out=outfile, pdffile=FALSE)
+
+# SERE coefficient calculation (Poisson hypothesis for replicates techiques), to know if the variability between the r├ęplicates or the conditons is hight or not. 
+coef <- pairwiseSERE(counts)
+print(coef)
+coef
+# Creation structure de donnees cds, !! we use newCountDataset because that we have first column not numeric, and DESeq dosen't take non numeric values.
+cds <- newCountDataSet( counts, target$group )
+
+# Diagnostic for clustering of non-normalized samples
+OUT_clusterPlot_before <- paste(OUT_imgDir, "clusteringOfSamplesBefore.png", sep="/")
+clusterPlot(cds, OUT_clusterPlot_before, out=outfile)
+
+
+# Normalisation (calcul des lib size factors )
+cds <- estimateSizeFactors( cds )
+
+# Estimation de la dispersion
+# parametres: 
+	# method: how samples are pooled to estimate dispersion. If no replicates use "blind"
+	# sharingMode: how variance estimate is computed with respect to the fitted line. 
+	# 				"Maximum" is the most conservative (max between fit and estimation), "fit-only" keeps the estimated value
+	# fitType: refers to the model. "Local" is the published model, "parametric" is glm-based (may not converge), now we use "parametric" as default value.
+#in this case, without replicates
+if(withOutReplicates!=0){
+	cds <- estimateDispersions( cds, sharingMode="fit-only", method="blind")
+} else if(withOutReplicates==0){
+	#cds <- estimateDispersions( cds, sharingMode="fit-only", fitType="local")}
+	cds <- estimateDispersions( cds)}
+# Analyse differentielle, ajustement BH par defaut
+res <- nbinomTest( cds, cond1, cond2)  
+
+# Diagnostic for clustering of normalized samples
+OUT_clusterPlot <- paste(OUT_imgDir, "clusteringOfSamples.png", sep="/")
+clusterPlot(cds, OUT_clusterPlot, out=outfile)
+
+# Control plot of dispersion estimates
+OUT_plotDispEstimatesName <- paste(OUT_imgDir, "disperssionEstimates.png", sep="/")
+plotDispEstimates( cds, OUT_plotDispEstimatesName, out=outfile )
+
+# Distribution of raw p-values
+OUT_histoRawpName <- paste(OUT_imgDir, "histoRawPvalue.png", sep="/")
+histoRawp( res, OUT_histoRawpName, out=outfile )
+
+# MAplot showing DE genes
+OUT_MAplotDEName <- paste(OUT_imgDir, "MAplotDE.png", sep="/")
+MAplotDE( res, alpha, OUT_MAplotDEName, out=outfile )
+
+# export complete data
+OUT_completeName <- args[9]
+complete <- exportComplete( counts, res, target, adjMethod, cond1, cond2, OUT_completeName, out=outfile )
+
+# export significant genes
+OUT_upName <- args[10]
+OUT_downName <- args[11]
+diff <- exportDiff( complete, alpha, adjMethod, OUT_upName, OUT_downName, out=outfile )
+
+# write all images results into an HTML file
+prefixHTMLname <- tab[length(tab)]
+#HTMLCSS(file.path(res_dir), filename=prefixHTMLname, CSSfile="R2HTML")
+HTMLInitFile(file.path(res_dir), filename=prefixHTMLname, BackGroundColor="white")
+HTML.title("<center>Differential Expression DESeq analysis.", HR=1) 
+HTML.title("<center>BarplotTC: number of RNA-seq reads per sample.", HR=2)
+    	HTMLInsertGraph("barplotTC.png")
+
+HTML.title("<center>BarplotNul: number of RNA-seq reads that the count is 0 (nul).", HR=2)
+	HTMLInsertGraph("barplotNul.png")
+
+HTML.title("<center>DensityPlot: density of each sample.", HR=2)
+	HTMLInsertGraph("densityPlot.png")
+
+HTML.title("<center>Boxplot: number of RNA-seq reads distribution per sample.", HR=2)
+	HTMLInsertGraph("boxplotCounts.png")
+
+HTML.title("<center>MajorSequence: the proportion of reads associated with the most expressed sequence.", HR=2)
+	HTMLInsertGraph("majSequence.png")
+
+HTML.title("<center>ScatterPlot: Scatter plot of samples.", HR=2)
+	HTMLInsertGraph("scatterPlot.png")
+
+HTML.title("<center>Clustering Of No-Normalized Samples: Representing the no-normalized samples in Diagnostic.", HR=2)	
+	HTMLInsertGraph("clusteringOfSamplesBefore.png")
+
+HTML.title("<center>Clustering Of Normalized Samples: Representing the normalized samples in Diagnostic.", HR=2)	
+	HTMLInsertGraph("clusteringOfSamples.png")
+
+HTML.title("<center>DispersionEstimates: representing dispersion estimates vs mean expression.", HR=2)
+	HTMLInsertGraph("disperssionEstimates.png")
+
+HTML.title("<center>HistoRawPValue: histogram of raw p-value.", HR=2)
+	HTMLInsertGraph("histoRawPvalue.png")
+
+HTML.title("<center>MAplotDE: the differentially expressed genes (red point).", HR=2)
+	HTMLInsertGraph("MAplotDE.png")
+HTMLEndFile()
+absoluPrefixHTMLname <- paste(res_dir, prefixHTMLname, sep="")
+outName <- paste(absoluPrefixHTMLname, ".html", sep="")
+# change name is to be adapted into Galaxy
+file.rename(outName, OUT_HTMLname)
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/barplotNul.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,19 @@
+# barplotNul
+# barplot representing null counts per sample
+
+# input : counts, target, projectName
+# output : barplotNul (png)
+
+# created Feb 7th, 2012
+# modified April 30th, 2012 (target$group instead of target)
+
+barplotNul <- function( counts, group,  OUT_barplotNulName, out = TRUE ){
+
+  if (out) png( file=OUT_barplotNulName )
+
+  N <- apply(counts, 2, function(x){sum(x == 0)})/nrow(counts)
+  barplot(N, col=as.integer(group)+1, main = "Proportion of null counts per Sample", ylim = c(0,1))
+  legend("topright", as.character(unique(group)), lty=1, col=as.integer(unique(group))+1)
+
+  if (out) dev.off()
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/barplotTC.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,20 @@
+# barplotTC
+# barplot representing total count per sample
+
+# input : counts, target, projectName
+# output : barplotTC (png)
+
+# created Feb 7th, 2012
+# modified April 30th, 2012 (group instead of target$group)
+
+barplotTC <- function( counts, group, OUT_barplotTCName, out = TRUE ){
+
+  if (out) png( file=OUT_barplotTCName )
+
+  ylim <- c(0, max(colSums(counts))*1.2)
+  barplot( colSums(counts), col=as.integer(group)+1, main = "Total Read Count per Sample",  ylim=ylim )
+  legend( "topright", as.character(unique(group)), lty=1,
+         col=as.integer(unique(group))+1 )
+
+  if (out) dev.off()
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/boxplotCounts.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,18 @@
+# boxplotCounts
+# boxplots representing counts distribution per sample
+
+# input : counts, target, projectName, type of data (raw or norm)
+# output : boxplot (png)
+
+# created Feb 7th, 2012
+# modified April 30th, 2012
+
+boxplotCounts <- function( counts, group, type = c("raw", "norm"), OUT_boxplotCountsName, out = TRUE ){
+
+  if (out) png( file=OUT_boxplotCountsName )
+
+  boxplot( log2(counts+1), col=as.integer(group)+1, main = paste(type[1], " counts distribution", sep="" ) )
+  legend( "topright", as.character(unique(group)), lty=1, col=as.integer(unique(group))+1 )
+
+  if (out) dev.off()
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/clusterPlot.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,27 @@
+# clusterPlot
+# dendrogram of sample clustering
+
+# input : counts, outputName, type of data (raw or norm)
+# output : dendrogram (jpeg)
+
+# created Sept 13th, 2012
+# modified Oct 30th, 2012
+# Marie-Agnes Dillies
+
+
+clusterPlot <- function( cds, OUT_clusterPlot, type = "raw", out = TRUE ){
+
+  if (out) png( file=OUT_clusterPlot )
+
+  if (type == "norm"){
+    cdsblind <- estimateDispersions( cds, method="blind" )
+    vsd <- getVarianceStabilizedData( cdsblind )
+  }
+  else {
+    vsd <- counts(cds)
+  }
+  hc <- hclust( dist(t(vsd)), method="ward" )
+  plot( hc, xlab = "Euclidean distance, Ward criterion", main=paste("Cluster Dendrogram, ", type, " data", sep="") )
+
+  if (out) dev.off()
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/densityPlot.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,23 @@
+# densityPlot
+# density plot of all samples
+
+# input : counts, target, projectName
+# output : densplot (png)
+
+# created Feb 7th, 2012
+# modified April 30th, 2012
+
+
+densityPlot <- function( counts, group, OUT_densityPlotName, out = TRUE ){
+
+  if (out) png( file=OUT_densityPlotName )
+
+  couleurs <- as.integer( group ) + 1
+  ylim <- c(0, max(density(log2(counts)+1)$y)*1.5)
+  plot( density(log2(counts[,1])+1), main="Density of counts distribution", col=couleurs[1], ylim = ylim )
+  for (i in 2:ncol(counts))
+  	lines( density(log2(counts[,i])+1), col=couleurs[i] )
+  legend( "topright", as.character(unique(group)), lty=1, col=as.integer(unique(group))+1 )
+
+  if (out) dev.off()
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/exportComplete.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,20 @@
+# exportComplete
+# export complete data and results
+
+# input : counts res, target
+# output : complete data and xls file (in text format)
+
+# created Feb 14th, 2012
+# modified March 9th, 2012 (order of cond1 and cond2)
+
+
+exportComplete <- function( counts, res, target, adjMethod, cond1, cond2, OUT_completeName, out = T ){
+	
+	complete <- data.frame( res$id, counts, res[,3:ncol(res)] )
+	colnames(complete) <- c( "id", as.character(target$label), cond2, cond1, "FC", "log2FC", "rawp", 
+							paste("adjp",adjMethod,sep="") )
+
+  if (out)
+  		write.table( complete, file=OUT_completeName, sep="\t", row.names=F )
+  return( complete )
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/exportDiff.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,42 @@
+# exportDiff
+# export differentially expressed genes
+
+# input : complete, alpha, adjMethod, projectName
+# output : diff genes, up and down in xls files
+
+# created Feb 14th, 2012
+
+
+exportDiff <- function( complete, alpha, adjMethod, OUT_upName, OUT_downName, out = T ){
+	
+	diff <- complete[which(complete[,grep("adjp",colnames(complete))] < alpha),]
+
+	gup <- up( diff )	
+	gdown <- down( diff )
+	
+  if (out){
+    gup[,(ncol(gup)-4):ncol(gup)] <- format( gup[,(ncol(gup)-4):ncol(gup)], digits=3, dec=",")
+    gdown[,(ncol(gdown)-4):ncol(gdown)] <- format( gdown[,(ncol(gdown)-4):ncol(gdown)], digits=3, dec=",")
+		write.table(gup, file=OUT_upName, row.names=F, sep="\t")
+		write.table(gdown, file=OUT_downName, row.names=F, sep="\t")
+  }	
+  return( diff )
+}
+
+
+up <- function( diff ){
+		
+	up <- diff[diff$log2FC > 0,]
+	up <- up[order(up[,grep("adjp",colnames(up))]),]
+
+	return( up )	
+}
+
+
+down <- function( diff ){
+		
+	down <- diff[diff$log2FC < 0,]
+	down <- down[order(down[,grep("adjp",colnames(down))]),]
+
+	return( down )	
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/histoRawp.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,18 @@
+# histoRawp
+# histogram of raw p-values
+
+# input : res, OUT_histoRawpName
+# output : histogram (png)
+
+
+histoRawp <- function( res, OUT_histoRawpName, out = TRUE ){
+
+  if (out) png( file=OUT_histoRawpName )
+  
+  ind <- grep("val", colnames(res))
+  hist( res[,ind], nclass=50, xlab="Raw p-values", main="", col="skyblue" )
+
+  if (out) dev.off()
+}
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/loadCountData.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,36 @@
+# loadCountData
+# loads counts, one file per lane
+# file names from target file
+
+# input : target
+# output : raw count table
+
+# created Feb 6th, 2012
+# modified May 2nd, 2012 (colnames -> target$label)
+# Marie-Agnes Dillies
+
+
+loadCountData <- function(target, header){
+
+  require(DESeq)
+  fileNames <- target$files
+
+if(header!=0){
+	#rawCounts <- read.table(as.character(paste(rawDir,target$files[1],sep="/")), sep="\t", header=TRUE)
+	rawCounts <- read.table(as.character(target$files[1],sep="/"), sep="\t", header=TRUE)
+} else if(header==0){
+	rawCounts <- read.table(as.character(target$files[1],sep="/"), sep="\t")}
+  
+  colnames(rawCounts) <- c("Id", as.character(target$label[1]))
+
+  for (i in 2:length(fileNames)){
+	if(header!=0){
+  		tmp <- read.table(as.character(target$files[i],sep="/"), sep="\t", header=TRUE)
+	} else if(header==0){
+		tmp <- read.table(as.character(target$files[i],sep="/"), sep="\t")}
+  	colnames(tmp) <- c("Id", as.character(target$label[i]))
+  	rawCounts <- merge(rawCounts, tmp, by="Id", all=T)
+  }
+  rawCounts[is.na(rawCounts)] <- 0
+  return(rawCounts)
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/loadTargetFile.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,17 @@
+# loadTargetFile
+# loads file containing sample info
+
+# input : targetFile Name
+# output : target
+
+# created Feb 6th, 2012
+# Marie-Agnes Dillies
+
+
+loadTargetFile <- function(targetFile, header){
+if(header!=0){
+  return(read.table(targetFile, header=T, sep="\t"))
+	}else if(header==0){
+  return(read.table(targetFile, sep="\t"))
+	}	
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/majSequence.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,26 @@
+# majSequence
+# compute proportion of reads associated with most expressed sequence
+
+# input : counts, target, projectName
+# output : barplot, % associated with majority gene
+
+# created Feb 7th, 2012
+# modified Feb 20th, 2012
+# modified April 30th, 2012
+# Marie-Agnes Dillies
+
+
+majSequence <- function( counts, group, OUT_majSequenceName, out = T, position = "topright" ){
+
+  if (out) png( file=OUT_majSequenceName )
+
+  maj <- apply(counts, 2, function(x){x <- x[order(x, decreasing=T)]; x[1]*100/sum(x)})
+  seqname <- apply(counts, 2, function(x){x <- x[order(x, decreasing=T)]; names(x)[1]})
+
+  x <- barplot( maj, col=as.integer(group)+1, main = "Proportion of reads from most expressed gene", 
+		ylim = c(0, max(maj)*1.2), cex.main=0.8 )
+  for (i in 1:length(seqname)) text( x[i], maj[i]/2, seqname[i], cex=0.8, srt=90, adj=0)
+  legend( position, as.character(unique(group)), lty=1, col=as.integer(unique(group))+1 )
+
+  if (out) dev.off()
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/pairwiseSERE.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,41 @@
+# pairwiseSERE
+# compute pairwise SERE statistics
+
+# input : counts
+# output : matrix of SERE values
+
+# created october 19th, 2012
+# Marie-Agnes Dillies
+
+
+pairwiseSERE <- function( counts ){
+  
+  sere <- matrix( NA, ncol=ncol(counts), nrow=ncol(counts) )
+  for (i in 1:ncol(counts)){
+    for (j in 1:ncol(counts)){
+      sere[i,j] <- sigfun_Pearson( counts[,c(i,j)] )
+    }
+  }
+  colnames(sere) <- rownames(sere) <- colnames(counts)
+  return( formatC(sere, format="f", digits=2) )
+}
+
+sigfun_Pearson <- function(observed) {
+  #calculate lambda and expected values
+  laneTotals<- colSums(observed);
+  total <- sum(laneTotals)
+  fullObserved <- observed[rowSums(observed)>0,];
+  fullLambda <- rowSums(fullObserved)/total;
+  fullLhat <- fullLambda > 0;
+  fullExpected<- outer(fullLambda, laneTotals);
+
+  #keep values
+  fullKeep <- which(fullExpected > 0);
+  
+  #calculate degrees of freedom (nrow*(ncol -1) >> number of parameters - calculated (just lamda is calculated >> thats why minus 1)
+  #calculate pearson and deviance for all values
+  oeFull <- (fullObserved[fullKeep] - fullExpected[fullKeep])^2/ fullExpected[fullKeep] # pearson chisq test
+  dfFull <- length(fullKeep) - sum(fullLhat!=0);
+  
+  return(c(sqrt(sum(oeFull)/dfFull)));
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/pairwiseScatterPlots.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,31 @@
+# pairwiseScatterPlots
+# scatter plots for pairwise comparaisons of log counts
+
+# input : counts, target, outputName
+# output : scatter plots (pdf: allows multiple figures in one file)
+
+# created Feb 21th, 2012
+# modified Sept 27th, 2012 (pdf output file)
+# modified Oct 30th, 2012 (png)
+# Marie-Agnes Dillies
+
+
+pairwiseScatterPlots <- function( counts, target, OUT_scatterPlot, out = TRUE, pdffile = FALSE ){
+
+  if (out & !pdffile) png( OUT_scatterPlot )
+  if (pdffile) pdf( OUT_scatterPlot )
+  
+  conds <- unique(target$group)
+  # colnames(counts) <- target$label
+  
+  for (i in 1:(length(conds)-1)){
+  	for (j in (i+1):length(conds)){
+  		cond1 <- conds[i]; cond2 <- conds[j]
+		pairs( log2(counts[, which(target$group %in% c(as.character(cond1), as.character(cond2)))]+1), 
+				pch=".", cex=0.5, main = paste(cond1, cond2, sep=" vs ") )
+  	}
+  }
+
+  if (pdffile) dev.off()
+  if (out) dev.off()
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/plotDispEstimates.R	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,21 @@
+# plotDispEstimates
+# scatter plots representing dispersion estimates vs mean expression
+
+# input : cds, OUT_plotDispEstimatesName
+# output : scatterplot (png)
+
+plotDispEstimates <- function( cds, OUT_plotDispEstimatesName, out = TRUE ){
+
+  if (out) png( file=OUT_plotDispEstimatesName )
+  
+  plot(
+  	rowMeans( counts(cds, normalized=T) ),
+  	fitInfo(cds)$perGeneDispEsts,
+  	pch=".", log="xy",
+  	xlab = "Mean expression strength", ylab = "Dispersion estimate" )
+  	
+  xg <- 10^seq(-.5, 5, length.out=300)
+  lines( xg, fitInfo(cds)$dispFun(xg), col="red" )
+
+  if (out) dev.off()
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/raw/f1cond1.tsv	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,18761 @@
+GliNS1	G144
+13CDNA73	4
+15E1.2	75
+182-FIP	118
+2'-PDE	39
+3'HEXO	18
+3.8-1	0
+384D8-2	3
+76P	61
+7h3	4
+8D6A	1
+A1BG	1
+A2BP1	19
+A2M	2724
+A4GALT	0
+A4GNT	0
+AAA1	2
+AAAS	57
+AACS	1904
+AADACL1	3
+AADAT	18
+AAK1	2
+AAMP	215
+AANAT	0
+AARS	157
+AARSD1	27
+AARSL	21
+AASDH	15
+AASDHPPT	162
+AASS	159
+AATF	68
+AATK	3
+ABAT	493
+ABC1	7
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