Changes between Version 9 and Version 10 of SnpAnnotationPipeline


Ignore:
Timestamp:
Nov 24, 2010 1:19:32 PM (14 years ago)
Author:
a.kanterakis
Comment:

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  • SnpAnnotationPipeline

    v9 v10  
     1= !PrepareGFFFilesFromBGIForSeattleSeqAnnotation==
     2Preprocesses 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.
     3
     4== Parameters ==
     5 * GFFFilename : Input filename
     6 * outputGFFFilename: Output filename
     7
     8== Example ==
     9{{{
     10#!div style="font-size: 80%"
     11Code highlighting:
     12  {{{#!python
     13PrepareGFFFilesFromBGIForSeattleSeqAnnotation("/Users/alexandroskanterakis/Data/CD_china/000057.snp.Q20.gff", "/Users/alexandroskanterakis/Data/CD_china/000057.snp.Q20.gff")
     14  }}}
     15}}}
     16
     17== Source Code ==
     18http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/PrepareGFFFilesFromBGIForSeattleSeqAnnotation.py
     19
    120= !AnnotateVarianListFileViaSeattleSeqAnnotation =
    221Annotate 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: