= PrepareGFFFilesFromBGIForSeattleSeqAnnotation = Preprocesses GFF files coming from the BGI institute for SeattleAnnotationTool. Replace `alleles` with `allele` and adds the line: `# autoFile testAuto.txt` in the top of the file. == Parameters == * GFFFilename : Input filename * outputGFFFilename: Output filename == Example == {{{ #!div style="font-size: 80%" Code highlighting: {{{#!python PrepareGFFFilesFromBGIForSeattleSeqAnnotation("/Users/alexandroskanterakis/Data/CD_china/000057.snp.Q20.gff", "/Users/alexandroskanterakis/Data/CD_china/000057.snp.Q20.gff") }}} }}} == Source Code == http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/PrepareGFFFilesFromBGIForSeattleSeqAnnotation.py = !AnnotateVarianListFileViaSeattleSeqAnnotation = Annotate Files with Variants through Seattle Seq Annotation: http://gvs.gs.washington.edu/SeattleSeqAnnotation/ . The java code that wraps the forms is provided from SeattleSeq Annotation: http://gvs.gs.washington.edu/SeattleSeqAnnotation/SubmitSeattleSeqAnnotationAutoJob.java . This method wraps the wrapper(..) and provides a python implementation. In order to run there should be a directory under the current path, named "jars" with the following jar files: * httpunit.jar * js-1.6R5.jar * junit-3.8.1.jar * nekohtml-0.9.5.jar * xercesImpl-2.6.1.jar == Parameters == For a complete list of parameters please check the [http://gvs.gs.washington.edu/SeattleSeqAnnotation/|SeattleSeq Annotation website] and the example below == Example == {{{ #!div style="font-size: 80%" Code highlighting: {{{#!python AnnotateVarianListFileViaSeattleSeqAnnotation( inputFile=/Users/alexandroskanterakis/Data/SNP/chr1.snp.Q20.gff, outputFile=/Users/alexandroskanterakis/Tools/annotation/seattleseqannotation/output.txt, eMail=alexandros.kanterakis@gmail.com, fileFormat=GFF, geneData=CCDS2008, allelesMaq=true, allelesDBSNP=true, scorePhastCons=true, scorePhastCons=true, consScoreGERP=true, chimpAllele=true, CNV=true, geneList=true, HapMapFreqType=HapMapFreqMinor, geneList=true, hasGenotypes=true, dbSNPValidation=true, repeats=true, geneList=true, proteinSequence=true, polyPhen=true, clinicalAssociation=true ) }}} }}} == Source Code == http://www.bbmriwiki.nl/svn/SequenceAnnotation/AnnotateVarianListFileViaSeattleSeqAnnotation/AnnotateVarianListFileViaSeattleSeqAnnotation.py = AddPolyphenAnnotationToSNPsFromSeattleSeqAnnotationOutputs = This method takes a list of files that have been generated from [http://gvs.gs.washington.edu/SeattleSeqAnnotation/ SeattleSeq Annotation] tool and a list of tabular files that contain Chromosome and position columns. It adds the [http://genetics.bwh.harvard.edu/pph/ polyphen] annotation that is contained in the former list of files to the later. == Parameters == * listOfSeattleSeqAnnotationOutputs: list of SeattleSeq Annotation files that we want to take the polyphen annotation from * listOfFileToBeAnnotated: List of files with chromosome and position information. * chromosomeColumn: The Chromosome column of the files to be annotated * positionColumn: The position column of the files to be annotated * outputDir: The directory where the generated files will be stored * outputSuffix: The suffix of the output files. == Example == {{{ #!div style="font-size: 80%" Code highlighting: {{{#!python listOfSeattleSeqAnnotationOutputs = [ "/Users/alexandroskanterakis/Data/CD_china/000057.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/000074.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/000159.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/000363.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/030042.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/030101.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/960313.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/960318.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0316-04.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0316-05.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0322-07.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0322-08.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0326-03.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0326-07.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0360-02.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0360-05.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0360-06.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0376-02.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0376-05.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0398-011.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD0398-012.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD2018-03.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD2018-06.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5000-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5059-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5063-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5065-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5066-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5067-005.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5084-007.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5096-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5116-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5166-005.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5174-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5176-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5217-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5252-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5257-005.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt", "/Users/alexandroskanterakis/Data/CD_china/CD5258-002.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt" ] filesToBeAnnotated = [ "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22.txt" ] AddPolyphenAnnotationToSNPsFromSeattleSeqAnnotationOutputs( listOfSeattleSeqAnnotationOutputs=listOfSeattleSeqAnnotationOutputs, listOfFileToBeAnnotated=filesToBeAnnotated, chromosomeColumn=2, positionColumn=3, outputDir="/Users/alexandroskanterakis/Data/CD_china/Intersection", outputSuffix="_poluphenExample.txt", numberOfFirstLinesToIgnore=1 ) }}} }}} == Source code == http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/AddPolyphenAnnotationToSNPsFromSeattleSeqAnnotationOutputs.py = AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl = Create Gene Ontology (http://www.geneontology.org/) annotation for a list of files that contain at least a position column and a chromosome column. == Parameters == * listOfFilesToAnnotate: Python list of filenames to be annotated * numberOfFirstLinesToIgnoreInFileToAnnotate: * chromosomeColumnOfFilesToAnnotate: The # of the chromosome column in the file to be annotated (starting from 0) * positionColumnOfFilesToAnnotate: The # of the position column in the file to be annotated (starting from 0) * resolveDuplicateValuesFunctionInFileToBeAnnotated: What should we do if we found 2 lines in the file to be annotated that has the same position and chromosome? If not set to None it will call the function assigned to this parameter * fileWithGOAnnotation: The file that has been downloaded from BioMart and contains the GO annotation. * fileWithGOAnnotationChromosomeColumn: The column that contain the chromosome in the fileWithGOAnnotation * fileWithGOAnnotationStartColumn: The column that contain the start of the transcript in the fileWithGOAnnotation * fileWithGOAnnotationEndColumn: The columns that contain the end of the transcript in the fileWithGOAnnotation * columnsWithGOAnnotationComaSeparated: The columns that contain the annotations that we want to add in the fileWithGOAnnotation. Example: "2,3,4" * numberOfFirstLinesToIgnoreInGOAnnotationFile * outputDirectory * outputSuffix: The output file will be: outputDirectory/(basename of inputFile)+outputSuffix == Example == {{{ #!div style="font-size: 80%" Code highlighting: {{{#!python fileList= [ "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22.txt" ] AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl( listOfFilesToAnnotate=fileList, numberOfFirstLinesToIgnoreInFileToAnnotate=1, chromosomeColumnOfFilesToAnnotate=2, positionColumnOfFilesToAnnotate=3, fileWithGOAnnotation="/Users/alexandroskanterakis/Data/Ensembl/GENE_START_END_GO_FROM_ENSEMBL_36.txt", fileWithGOAnnotationChromosomeColumn=1, fileWithGOAnnotationStartColumn=2, fileWithGOAnnotationEndColumn=3, columnsWithGOAnnotationComaSeparated="4,5,6,7,8,9", numberOfFirstLinesToIgnoreInGOAnnotationFile=1, outputDirectory="/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02", outputSuffix="_GO.txt" ) }}} }}} == Source Code == http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl.py = CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames = Creates Allele Frequency annotation from a list of VCFFilenames for tabular files that contain at least a chromosome and a position column. It requires the xapian (http://xapian.org) python package and vcftools (http://vcftools.sourceforge.net/) == Parameters == * pathToVCFTools: Path where vcftools is installed * listOfVCFFiles: python list of VCF files where the annotation will come from * listOfFilenamesToBeAnnotated * outputPreffix * xapianIndexDirectory. If None it will create a system temporary directory. == Example == {{{ #!div style="font-size: 80%" Code highlighting: {{{#!python import wikipl from wikipl import CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames VCFFilenames_Example = [ "/Users/alexandroskanterakis/Data/1000GP/vol1.ftp.pilot_data.release.2010_07.exon.snps/CEU.exon.2010_03.genotypes.vcf", "/Users/alexandroskanterakis/Data/1000GP/vol1.ftp.pilot_data.release.2010_07.exon.snps/YRI.exon.2010_03.genotypes.vcf" ] filesToBeAnnotated = [ "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22.txt" ] CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames( pathToVCFTools = "/Users/alexandroskanterakis/Tools/vcftools/cpp/vcftools", listOfVCFFiles=VCFFilenames_Example, listOfFilenamesToBeAnnotated=filesToBeAnnotated, outputPreffix="_AlleleFrequencyExample.txt", xapianIndexDirectory="/Users/alexandroskanterakis/Data/CD_china/Intersection/xapianDB_Example" ) }}} }}} == Source code == http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames.py = MergeHorizontallyFilesAccordingToCommonColumns = Merge horizontally files according to common columns == Parameters == * listOfFilenamesToBeAnnotated: Python list of filenames to be annotated. * listOfColumnsFromFileToBeAnnotated: Python list of columns that we want to keep from the files to be annotated * listOfListsOfInputFilenames: Python list of python list of input filenames * listOfAnnotationFileColumns * listOfFirstLinesToIgnore: Python list of first lines to ignore from each annotation file * listOfOutputFilenames == Example == {{{ #!div style="font-size: 80%" Code highlighting: {{{#!python filesToBeAnnotated = [ "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22.txt" ] filesAnnotation1 = [ "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21_polyphen.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22_polyphen.txt" ] filesAnnotation2 = [ "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21_GO.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22_GO.txt" ] filesAnnotation3 = [ "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21_AlleleFrequency.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22_AlleleFrequency.txt" ] filesOutput123Annotated = [ "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21_Annotated.txt", "/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22_Annotated.txt" ] MergeHorizontallyFilesAccordingToCommonColumns( listOfFilenamesToBeAnnotated=filesToBeAnnotated, # listOfColumnsFromFileToBeAnnotated=range(39), listOfColumnsFromFileToBeAnnotated = [2,3], listOfListsOfInputFilenames=[filesAnnotation1,filesAnnotation2,filesAnnotation3], listOfAnnotationFileColumns=[[2],[2,3,4,5,6,7],[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25]], listOfOutputFilenames=filesOutput123Annotated ) }}} }}} == Source Code == http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/MergeHorizontallyFilesAccordingToCommonColumns.py = Pipeline Elements = This section will describe all parts of our annotation pipeline, the scripts have, and the features it will return. ||'''script'''||'''feature'''||'''description'''||'''source'''|| ||1KGannotation.py||alleleFreq||allele freq in 1KG||1KG|| ||TODO|||||||| |||||||||| = End of Pipeline = = Related work = * http://www.svaproject.org/ * http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001074