Changes between Version 13 and Version 14 of SnpAnnotationPipeline

Timestamp:

Nov 24, 2010 2:11:29 PM (15 years ago)

Author:

a.kanterakis

Comment:

--

SnpAnnotationPipeline

@@ -162 +162 @@
 == Source code ==
 http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/AddPolyphenAnnotationToSNPsFromSeattleSeqAnnotationOutputs.py
+
+= AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl =
+Create Gene Ontology (http://www.geneontology.org/) annotation for a list of files that contain at least a position column and a chromosome column. 
+
+== Parameters ==
+ * listOfFilesToAnnotate: Python list of filenames to be annotated
+ * numberOfFirstLinesToIgnoreInFileToAnnotate: 
+ * chromosomeColumnOfFilesToAnnotate: The # of the chromosome column in the file to be annotated (starting from 0)
+ * positionColumnOfFilesToAnnotate: The # of the position column in the file to be annotated (starting from 0)
+ * resolveDuplicateValuesFunctionInFileToBeAnnotated: What should we do if we found 2 lines in the file to be annotated that has the same position and chromosome? If not set to None it will call the function assigned to this parameter
+ * fileWithGOAnnotation: The file that has been downloaded from BioMart and contains the GO annotation. 
+ * fileWithGOAnnotationChromosomeColumn: The column that contain the chromosome in the fileWithGOAnnotation
+ * fileWithGOAnnotationStartColumn: The column that contain the start of the transcript in the fileWithGOAnnotation
+ * fileWithGOAnnotationEndColumn: The columns that contain the end of the transcript in the fileWithGOAnnotation
+ * columnsWithGOAnnotationComaSeparated: The columns that contain the annotations that we want to add in the fileWithGOAnnotation. Example: "2,3,4"
+ * numberOfFirstLinesToIgnoreInGOAnnotationFile
+ * outputDirectory
+ * outputSuffix: The output file will be: outputDirectory/(basename of inputFile)+outputSuffix
+
+== Example ==
+{{{
+#!div style="font-size: 80%"
+Code highlighting:
+  {{{#!python
+fileList= [
+"/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"
+]
+
+AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl(
+        listOfFilesToAnnotate=fileList,
+        numberOfFirstLinesToIgnoreInFileToAnnotate=1,
+        chromosomeColumnOfFilesToAnnotate=2,
+        positionColumnOfFilesToAnnotate=3,
+        fileWithGOAnnotation="/Users/alexandroskanterakis/Data/Ensembl/GENE_START_END_GO_FROM_ENSEMBL_36.txt",
+        fileWithGOAnnotationChromosomeColumn=1,
+        fileWithGOAnnotationStartColumn=2,
+        fileWithGOAnnotationEndColumn=3,
+        columnsWithGOAnnotationComaSeparated="4,5,6,7,8,9",
+        numberOfFirstLinesToIgnoreInGOAnnotationFile=1,
+        outputDirectory="/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02",
+        outputSuffix="_GO.txt"
+        )
+  }}}
+}}}
+
+== Source Code ==
+http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl.py
 = Pipeline Elements =