Changes between Version 13 and Version 14 of ImputationPipeline

Timestamp:

Nov 23, 2010 12:32:26 PM (14 years ago)

Author:

a.kanterakis

Comment:

--

ImputationPipeline

@@ -173 +173 @@
 ==== Source code ====
 http://www.bbmriwiki.nl/svn/Imputation/impute2/DividePedMapToChromosomes.py
+
+=== ConvertListsOfPedAndMapFilesToGenAndSample ===
+Converts 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.
+
+==== Parameters ====
+ * gtoolPath : Path to gtool (example: /Users/alexandroskanterakis/Tools/gtool/gtool)
+ * pedInputListOfFiles : Python list of input ped files
+ * mapInputListOfFiles : Python list of input map files
+ * sampleOutputListOfFiles : Python list of output sample files
+ * genOutputListOfFiles : Python list of output gen files
+
+==== Example ====
+
+{{{
+#!div style="font-size: 80%"
+Code highlighting:
+  {{{#!python
+output_divided_path = "/path/to/output/files"
+suffix = "_chr"
+
+ConvertListsOfPedAndMapFilesToGenAndSample(
+                gtoolPath = "/Users/alexandroskanterakis/Tools/gtool/gtool",
+                pedInputListOfFiles= [output_divided_path+ "/" + suffix + "_" + str(x) + ".ped" for x in range(1,22)+['X', 'Y']],
+                mapInputListOfFiles=[output_divided_path+ "/" + suffix + "_" + str(x) + ".map" for x in range(1,22)+['X', 'Y']],
+                sampleOutputListOfFiles=[output_divided_path+ "/" + suffix + "_" + str(x) + ".sample" for x in range(1,22)+['X', 'Y']],
+                genOutputListOfFiles=[output_divided_path+ "/" + suffix + "_" + str(x) + ".gen" for x in range(1,22)+['X', 'Y']]
+                )
+  }}}
+}}}
+
+==== Source code ====
+http://www.bbmriwiki.nl/svn/Imputation/impute2/ConvertListsOfPedAndMapFilesToGenAndSample.py
 == BEABLE pipeline ==