Changes between Version 14 and Version 15 of SnpAnnotationPipeline

Timestamp:

Nov 24, 2010 2:28:01 PM (14 years ago)

Author:

a.kanterakis

Comment:

--

SnpAnnotationPipeline

@@ -230 +230 @@
 == 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
 = Pipeline Elements =