Changes between Version 15 and Version 16 of SnpAnnotationPipeline


Ignore:
Timestamp:
Nov 24, 2010 2:35:33 PM (15 years ago)
Author:
a.kanterakis
Comment:

--

Legend:

Unmodified
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  • SnpAnnotationPipeline

    v15 v16  
    290290== Source code ==
    291291http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames.py
     292
     293= MergeHorizontallyFilesAccordingToCommonColumns =
     294Merge horizontally files according to common columns
     295
     296== Parameters ==
     297 * listOfFilenamesToBeAnnotated: Python list of filenames to be annotated.
     298 * listOfColumnsFromFileToBeAnnotated: Python list of columns that we want to keep from the files to be annotated
     299 * listOfListsOfInputFilenames: Python list of python list of input filenames
     300 * listOfAnnotationFileColumns
     301 * listOfFirstLinesToIgnore: Python list of first lines to ignore from each annotation file
     302 * listOfOutputFilenames
     303
     304== Example ==
     305{{{
     306#!div style="font-size: 80%"
     307Code highlighting:
     308  {{{#!python
     309filesToBeAnnotated = [
     310"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1.txt",
     311"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2.txt",
     312"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3.txt",
     313"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4.txt",
     314"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5.txt",
     315"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6.txt",
     316"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7.txt",
     317"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8.txt",
     318"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9.txt",
     319"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10.txt",
     320"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11.txt",
     321"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12.txt",
     322"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13.txt",
     323"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14.txt",
     324"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15.txt",
     325"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16.txt",
     326"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17.txt",
     327"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18.txt",
     328"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19.txt",
     329"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20.txt",
     330"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21.txt",
     331"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22.txt"
     332]
     333
     334filesAnnotation1 = [
     335"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1_polyphen.txt",
     336"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2_polyphen.txt",
     337"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3_polyphen.txt",
     338"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4_polyphen.txt",
     339"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5_polyphen.txt",
     340"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6_polyphen.txt",
     341"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7_polyphen.txt",
     342"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8_polyphen.txt",
     343"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9_polyphen.txt",
     344"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10_polyphen.txt",
     345"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11_polyphen.txt",
     346"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12_polyphen.txt",
     347"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13_polyphen.txt",
     348"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14_polyphen.txt",
     349"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15_polyphen.txt",
     350"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16_polyphen.txt",
     351"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17_polyphen.txt",
     352"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18_polyphen.txt",
     353"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19_polyphen.txt",
     354"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20_polyphen.txt",
     355"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21_polyphen.txt",
     356"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22_polyphen.txt"
     357]
     358
     359filesAnnotation2 = [
     360"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1_GO.txt",
     361"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2_GO.txt",
     362"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3_GO.txt",
     363"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4_GO.txt",
     364"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5_GO.txt",
     365"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6_GO.txt",
     366"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7_GO.txt",
     367"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8_GO.txt",
     368"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9_GO.txt",
     369"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10_GO.txt",
     370"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11_GO.txt",
     371"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12_GO.txt",
     372"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13_GO.txt",
     373"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14_GO.txt",
     374"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15_GO.txt",
     375"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16_GO.txt",
     376"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17_GO.txt",
     377"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18_GO.txt",
     378"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19_GO.txt",
     379"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20_GO.txt",
     380"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21_GO.txt",
     381"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22_GO.txt"
     382]
     383
     384filesAnnotation3 = [
     385"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1_AlleleFrequency.txt",
     386"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2_AlleleFrequency.txt",
     387"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3_AlleleFrequency.txt",
     388"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4_AlleleFrequency.txt",
     389"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5_AlleleFrequency.txt",
     390"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6_AlleleFrequency.txt",
     391"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7_AlleleFrequency.txt",
     392"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8_AlleleFrequency.txt",
     393"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9_AlleleFrequency.txt",
     394"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10_AlleleFrequency.txt",
     395"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11_AlleleFrequency.txt",
     396"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12_AlleleFrequency.txt",
     397"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13_AlleleFrequency.txt",
     398"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14_AlleleFrequency.txt",
     399"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15_AlleleFrequency.txt",
     400"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16_AlleleFrequency.txt",
     401"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17_AlleleFrequency.txt",
     402"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18_AlleleFrequency.txt",
     403"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19_AlleleFrequency.txt",
     404"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20_AlleleFrequency.txt",
     405"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21_AlleleFrequency.txt",
     406"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22_AlleleFrequency.txt"
     407]
     408
     409filesOutput123Annotated = [
     410
     411"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_1_Annotated.txt",
     412"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_2_Annotated.txt",
     413"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_3_Annotated.txt",
     414"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_4_Annotated.txt",
     415"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_5_Annotated.txt",
     416"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_6_Annotated.txt",
     417"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_7_Annotated.txt",
     418"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_8_Annotated.txt",
     419"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_9_Annotated.txt",
     420"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_10_Annotated.txt",
     421"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_11_Annotated.txt",
     422"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_12_Annotated.txt",
     423"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_13_Annotated.txt",
     424"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_14_Annotated.txt",
     425"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_15_Annotated.txt",
     426"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_16_Annotated.txt",
     427"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_17_Annotated.txt",
     428"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_18_Annotated.txt",
     429"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_19_Annotated.txt",
     430"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_20_Annotated.txt",
     431"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_21_Annotated.txt",
     432"/Users/alexandroskanterakis/Data/CD_china/genomeWideExcluding/genomeWideExcluding360-02/tab_22_Annotated.txt"
     433
     434]
     435
     436MergeHorizontallyFilesAccordingToCommonColumns(
     437        listOfFilenamesToBeAnnotated=filesToBeAnnotated,
     438#       listOfColumnsFromFileToBeAnnotated=range(39),
     439        listOfColumnsFromFileToBeAnnotated = [2,3],
     440        listOfListsOfInputFilenames=[filesAnnotation1,filesAnnotation2,filesAnnotation3],
     441        listOfAnnotationFileColumns=[[2],[2,3,4,5,6,7],[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25]],
     442        listOfOutputFilenames=filesOutput123Annotated
     443        )
     444  }}}
     445}}}
     446
     447== Source Code ==
     448http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/MergeHorizontallyFilesAccordingToCommonColumns.py
    292449= Pipeline Elements =
    293450