wiki:SnpAnnotationPipeline

Context Navigation

Version 15 (modified by a.kanterakis, 15 years ago) (diff)
--

PrepareGFFFilesFromBGIForSeattleSeqAnnotation

Preprocesses 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.

Parameters

GFFFilename : Input filename
outputGFFFilename: Output filename

Example

Code highlighting:

PrepareGFFFilesFromBGIForSeattleSeqAnnotation("/Users/alexandroskanterakis/Data/CD_china/000057.snp.Q20.gff", "/Users/alexandroskanterakis/Data/CD_china/000057.snp.Q20.gff")

Source Code

http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/PrepareGFFFilesFromBGIForSeattleSeqAnnotation.py

AnnotateVarianListFileViaSeattleSeqAnnotation

Annotate 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:

httpunit.jar
js-1.6R5.jar
junit-3.8.1.jar
nekohtml-0.9.5.jar
xercesImpl-2.6.1.jar

Parameters

For a complete list of parameters please check the Annotation website and the example below

Example

Code highlighting:

AnnotateVarianListFileViaSeattleSeqAnnotation(
        inputFile=/Users/alexandroskanterakis/Data/SNP/chr1.snp.Q20.gff,
        outputFile=/Users/alexandroskanterakis/Tools/annotation/seattleseqannotation/output.txt,
        eMail=alexandros.kanterakis@gmail.com,
        fileFormat=GFF,
        geneData=CCDS2008,
        allelesMaq=true,
        allelesDBSNP=true,
        scorePhastCons=true,
        scorePhastCons=true,
        consScoreGERP=true,
        chimpAllele=true,
        CNV=true,
        geneList=true,
        HapMapFreqType=HapMapFreqMinor,
        geneList=true,
        hasGenotypes=true,
        dbSNPValidation=true,
        repeats=true,
        geneList=true,
        proteinSequence=true,
        polyPhen=true,
        clinicalAssociation=true
        )

Source Code

http://www.bbmriwiki.nl/svn/SequenceAnnotation/AnnotateVarianListFileViaSeattleSeqAnnotation/AnnotateVarianListFileViaSeattleSeqAnnotation.py

AddPolyphenAnnotationToSNPsFromSeattleSeqAnnotationOutputs

This method takes a list of files that have been generated from SeattleSeq Annotation tool and a list of tabular files that contain Chromosome and position columns. It adds the polyphen annotation that is contained in the former list of files to the later.

Parameters

listOfSeattleSeqAnnotationOutputs: list of SeattleSeq? Annotation files that we want to take the polyphen annotation from
listOfFileToBeAnnotated: List of files with chromosome and position information.
chromosomeColumn: The Chromosome column of the files to be annotated
positionColumn: The position column of the files to be annotated
outputDir: The directory where the generated files will be stored
outputSuffix: The suffix of the output files.

Example

Code highlighting:

listOfSeattleSeqAnnotationOutputs = [
"/Users/alexandroskanterakis/Data/CD_china/000057.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/000074.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/000159.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/000363.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/030042.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/030101.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/960313.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/960318.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0316-04.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0316-05.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0322-07.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0322-08.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0326-03.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0326-07.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0360-02.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0360-05.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0360-06.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0376-02.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0376-05.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0398-011.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD0398-012.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD2018-03.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD2018-06.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5000-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5059-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5063-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5065-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5066-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5067-005.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5084-007.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5096-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5116-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5166-005.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5174-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5176-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5217-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5252-001.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5257-005.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt",
"/Users/alexandroskanterakis/Data/CD_china/CD5258-002.snp.Q20.alleleCorrection.autoFile.SeattleOutput.txt"
]

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"
]


AddPolyphenAnnotationToSNPsFromSeattleSeqAnnotationOutputs(
        listOfSeattleSeqAnnotationOutputs=listOfSeattleSeqAnnotationOutputs,
        listOfFileToBeAnnotated=filesToBeAnnotated,
        chromosomeColumn=2,
        positionColumn=3,
        outputDir="/Users/alexandroskanterakis/Data/CD_china/Intersection",
        outputSuffix="_poluphenExample.txt",
        numberOfFirstLinesToIgnore=1
        )

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

Code highlighting:

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

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

Code highlighting:

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

This section will describe all parts of our annotation pipeline, the scripts have, and the features it will return.

script	feature	description	source
1KGannotation.py	alleleFreq	allele freq in 1KG	1KG
TODO

End of Pipeline

Related work

Attachments (2)

AnnotateIntersectionOverview.zip (760.6 KB) - added by Patrick Deelen 15 years ago. Netbeans project for Annotation tool
lib.zip (693.7 KB) - added by Patrick Deelen 15 years ago. lib for AnnotateIntersectionOverview?

Download all attachments as: .zip

Download in other formats:

Plain Text