Changes between Version 13 and Version 14 of ImputationPipeline


Ignore:
Timestamp:
Nov 23, 2010 12:32:26 PM (11 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationPipeline

    v13 v14  
    173173==== Source code ====
    174174http://www.bbmriwiki.nl/svn/Imputation/impute2/DividePedMapToChromosomes.py
     175
     176=== ConvertListsOfPedAndMapFilesToGenAndSample ===
     177Converts many Ped and Map genotype files usually used by [http://pngu.mgh.harvard.edu/~purcell/plink/ plink] to gen and sample files usually used by [http://mathgen.stats.ox.ac.uk/impute/impute.html impute], [http://www.stats.ox.ac.uk/~marchini/software/gwas/chiamo.html chiamo], [http://www.stats.ox.ac.uk/~marchini/software/gwas/hapgen.html hapgen] and [http://www.stats.ox.ac.uk/~marchini/software/gwas/snptest.html snptest]. The conversion tool that is used is [http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html gtool]. All Python lists have to have the same size.
     178
     179==== Parameters ====
     180 * gtoolPath : Path to gtool (example: /Users/alexandroskanterakis/Tools/gtool/gtool)
     181 * pedInputListOfFiles : Python list of input ped files
     182 * mapInputListOfFiles : Python list of input map files
     183 * sampleOutputListOfFiles : Python list of output sample files
     184 * genOutputListOfFiles : Python list of output gen files
     185
     186==== Example ====
     187
     188{{{
     189#!div style="font-size: 80%"
     190Code highlighting:
     191  {{{#!python
     192output_divided_path = "/path/to/output/files"
     193suffix = "_chr"
     194
     195ConvertListsOfPedAndMapFilesToGenAndSample(
     196                gtoolPath = "/Users/alexandroskanterakis/Tools/gtool/gtool",
     197                pedInputListOfFiles= [output_divided_path+ "/" + suffix + "_" + str(x) + ".ped" for x in range(1,22)+['X', 'Y']],
     198                mapInputListOfFiles=[output_divided_path+ "/" + suffix + "_" + str(x) + ".map" for x in range(1,22)+['X', 'Y']],
     199                sampleOutputListOfFiles=[output_divided_path+ "/" + suffix + "_" + str(x) + ".sample" for x in range(1,22)+['X', 'Y']],
     200                genOutputListOfFiles=[output_divided_path+ "/" + suffix + "_" + str(x) + ".gen" for x in range(1,22)+['X', 'Y']]
     201                )
     202  }}}
     203}}}
     204
     205==== Source code ====
     206http://www.bbmriwiki.nl/svn/Imputation/impute2/ConvertListsOfPedAndMapFilesToGenAndSample.py
    175207== BEABLE pipeline ==
    176208