Changes between Version 14 and Version 15 of SnpAnnotationPipeline


Ignore:
Timestamp:
Nov 24, 2010 2:28:01 PM (11 years ago)
Author:
a.kanterakis
Comment:

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  • SnpAnnotationPipeline

    v14 v15  
    230230== Source Code ==
    231231http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl.py
     232
     233= CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames =
     234Creates 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/)
     235== Parameters ==
     236 * pathToVCFTools: Path where vcftools is installed
     237 * listOfVCFFiles: python list of VCF files where the annotation will come from
     238 * listOfFilenamesToBeAnnotated
     239 * outputPreffix
     240 * xapianIndexDirectory. If None it will create a system temporary directory.
     241
     242== Example ==
     243{{{
     244#!div style="font-size: 80%"
     245Code highlighting:
     246  {{{#!python
     247import wikipl
     248from wikipl import CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames
     249
     250VCFFilenames_Example = [
     251"/Users/alexandroskanterakis/Data/1000GP/vol1.ftp.pilot_data.release.2010_07.exon.snps/CEU.exon.2010_03.genotypes.vcf",
     252"/Users/alexandroskanterakis/Data/1000GP/vol1.ftp.pilot_data.release.2010_07.exon.snps/YRI.exon.2010_03.genotypes.vcf"
     253]
     254
     255filesToBeAnnotated = [
     256"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1.txt",
     257"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2.txt",
     258"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3.txt",
     259"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4.txt",
     260"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5.txt",
     261"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6.txt",
     262"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7.txt",
     263"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8.txt",
     264"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9.txt",
     265"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10.txt",
     266"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11.txt",
     267"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12.txt",
     268"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13.txt",
     269"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14.txt",
     270"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15.txt",
     271"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16.txt",
     272"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17.txt",
     273"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18.txt",
     274"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19.txt",
     275"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20.txt",
     276"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21.txt",
     277"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22.txt"
     278]
     279
     280CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames(
     281        pathToVCFTools = "/Users/alexandroskanterakis/Tools/vcftools/cpp/vcftools",
     282        listOfVCFFiles=VCFFilenames_Example,
     283        listOfFilenamesToBeAnnotated=filesToBeAnnotated,
     284        outputPreffix="_AlleleFrequencyExample.txt",
     285        xapianIndexDirectory="/Users/alexandroskanterakis/Data/CD_china/Intersection/xapianDB_Example"
     286        )
     287  }}}
     288}}}
     289
     290== Source code ==
     291http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames.py
    232292= Pipeline Elements =
    233293