Changes between Version 13 and Version 14 of SnpAnnotationPipeline


Ignore:
Timestamp:
Nov 24, 2010 2:11:29 PM (11 years ago)
Author:
a.kanterakis
Comment:

--

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  • SnpAnnotationPipeline

    v13 v14  
    162162== Source code ==
    163163http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/AddPolyphenAnnotationToSNPsFromSeattleSeqAnnotationOutputs.py
     164
     165= AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl =
     166Create Gene Ontology (http://www.geneontology.org/) annotation for a list of files that contain at least a position column and a chromosome column.
     167
     168== Parameters ==
     169 * listOfFilesToAnnotate: Python list of filenames to be annotated
     170 * numberOfFirstLinesToIgnoreInFileToAnnotate:
     171 * chromosomeColumnOfFilesToAnnotate: The # of the chromosome column in the file to be annotated (starting from 0)
     172 * positionColumnOfFilesToAnnotate: The # of the position column in the file to be annotated (starting from 0)
     173 * 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
     174 * fileWithGOAnnotation: The file that has been downloaded from BioMart and contains the GO annotation.
     175 * fileWithGOAnnotationChromosomeColumn: The column that contain the chromosome in the fileWithGOAnnotation
     176 * fileWithGOAnnotationStartColumn: The column that contain the start of the transcript in the fileWithGOAnnotation
     177 * fileWithGOAnnotationEndColumn: The columns that contain the end of the transcript in the fileWithGOAnnotation
     178 * columnsWithGOAnnotationComaSeparated: The columns that contain the annotations that we want to add in the fileWithGOAnnotation. Example: "2,3,4"
     179 * numberOfFirstLinesToIgnoreInGOAnnotationFile
     180 * outputDirectory
     181 * outputSuffix: The output file will be: outputDirectory/(basename of inputFile)+outputSuffix
     182
     183== Example ==
     184{{{
     185#!div style="font-size: 80%"
     186Code highlighting:
     187  {{{#!python
     188fileList= [
     189"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1.txt",
     190"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2.txt",
     191"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3.txt",
     192"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4.txt",
     193"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5.txt",
     194"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6.txt",
     195"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7.txt",
     196"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8.txt",
     197"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9.txt",
     198"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10.txt",
     199"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11.txt",
     200"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12.txt",
     201"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13.txt",
     202"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14.txt",
     203"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15.txt",
     204"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16.txt",
     205"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17.txt",
     206"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18.txt",
     207"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19.txt",
     208"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20.txt",
     209"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21.txt",
     210"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22.txt"
     211]
     212
     213AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl(
     214        listOfFilesToAnnotate=fileList,
     215        numberOfFirstLinesToIgnoreInFileToAnnotate=1,
     216        chromosomeColumnOfFilesToAnnotate=2,
     217        positionColumnOfFilesToAnnotate=3,
     218        fileWithGOAnnotation="/Users/alexandroskanterakis/Data/Ensembl/GENE_START_END_GO_FROM_ENSEMBL_36.txt",
     219        fileWithGOAnnotationChromosomeColumn=1,
     220        fileWithGOAnnotationStartColumn=2,
     221        fileWithGOAnnotationEndColumn=3,
     222        columnsWithGOAnnotationComaSeparated="4,5,6,7,8,9",
     223        numberOfFirstLinesToIgnoreInGOAnnotationFile=1,
     224        outputDirectory="/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02",
     225        outputSuffix="_GO.txt"
     226        )
     227  }}}
     228}}}
     229
     230== Source Code ==
     231http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl.py
    164232= Pipeline Elements =
    165233