= 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 = 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