= !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 = 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