Creating subset of a file based on specific columns Post: 302821927

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Top Forums Shell Programming and Scripting Creating subset of a file based on specific columns Post 302821927 by smitra on Sunday 16th of June 2013 06:38:42 AM

06-16-2013

Registered User

My Data is e.g.:

Code:

   Sample.Name                      Marker  RE Dye Allele.1 Size.1 Height.1 Peak.Area.1 Data.Point.1 Allele.2 Size.2 Height.2 Peak.Area.2 Data.Point.2
1       D71I1A  _Internal_Marker_Dye_Blue_ ALU   B        0     NA       NA          NA           NA        0     NA       NA          NA           NA
2       D71I1A _Internal_Marker_Dye_Green_ ALU   G        0     NA       NA          NA           NA        0     NA       NA          NA           NA
3       D71I1A  _Internal_Marker_Dye_Blue_ BSU   B        0     NA       NA          NA           NA        0     NA       NA          NA           NA
4       D71I1A _Internal_Marker_Dye_Green_ BSU   G        0     NA       NA          NA           NA        0     NA       NA          NA           NA
5       D71I1B  _Internal_Marker_Dye_Blue_ ALU   B        0     NA       NA          NA           NA        0  55.54       20         211         1576
6       D71I1B _Internal_Marker_Dye_Green_ ALU   G        0     NA       NA          NA           NA        0     NA       NA          NA           NA
7       D71I1B  _Internal_Marker_Dye_Blue_ BSU   B        0     NA       NA          NA           NA        0     NA       NA          NA           NA
8       D71I1B _Internal_Marker_Dye_Green_ BSU   G        0     NA       NA          NA           NA        0     NA       NA          NA           NA
9       D71I1C  _Internal_Marker_Dye_Blue_ ALU   B        0     NA       NA          NA           NA        0  55.38       18         192         1554
10      D71I1C _Internal_Marker_Dye_Green_ ALU   G        0     NA       NA          NA           NA        0     NA       NA          NA           NA

And I want a output like:

Code:

  Peak.Area.1 Peak.Area.2
1           NA          NA
2           NA          NA
3           NA          NA
4           NA          NA
5           NA         211
6           NA          NA
7           NA          NA
8           NA          NA
9           NA         192
10          NA          NA

But this is just an example.. I want it for a big file where there are over 1000 columns... thus I can't specify column 8 and 13 like in this example.
But I want to use the name Peak.Area.1,Peak.Area.2,Peak.Area.3 etc...something like Peak.Area.*.
Thanks,
Mitra

smitra

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LEARN ABOUT DEBIAN

svm-subset

svm-subset(1)							   User Manuals 						     svm-subset(1)

NAME

       svm-subset - a subset selection tool for LIBSVM

SYNOPSIS

       svm-subset [ -s method ] dataset number [ output1 ] [ output2 ]

DESCRIPTION

       Training  large data is time consuming. Sometimes one should work on a smaller subset first. The python script subset.py randomly selects a
       specified number of samples. For classification data, we provide a stratified selection to ensure the same class distribution in  the  sub-
       set.

OPTIONS

       -s method

       0      -- stratified selection (classification only) (default)

       1      -- random selection

       output1
	      The subset. If output1 is omitted, the subset will be printed on the screen.

       output2
	      The rest of data.

FILES

       See svm-train(1) for the format of dataset

EXAMPLES

	      svm-subset heart_scale 100 file1 file2

       From heart_scale 100 samples are randomly selected and stored in file1. All remaining instances are stored in file2.

BUGS

       Please report bugs to the Debian BTS.

AUTHOR

       Chih-Chung Chang, Chih-Jen Lin <cjlin@csie.ntu.edu.tw>, Chen-Tse Tsai <ctse.tsai@gmail.com> (packaging)

SEE ALSO

       svm-train(1), svm-predict(1)

Linux								     DEC 2009							     svm-subset(1)

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