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Full Discussion: Loop over awk or passing parameter
Top Forums Shell Programming and Scripting Loop over awk or passing parameter Post 302927293 by fat on Tuesday 2nd of December 2014 02:19:41 AM
Old 12-02-2014
Loop over awk or passing parameter
I wrote this script which works well when I manually input 55518622 and 1
but I need this script to be generic and loop over the following table
Code:
awk '$4>(55518622-500000) && $4<(55518622+500000)' chr1_GEN2bim | awk 'BEGIN {min=1000000000; max=0;}; {\
 if($4<min && $4 != "") min = $4; if($4>max && $4 != "") max = $4; } END {print "chr"$1"\t"min"\t"max}'


Given
Code:
1       55518622        rs45613943      1.983654e-08
1       109815252       rs611917        3.439871e-11
2       98323821        kgp8891906      3.619327e-19
10      15912165        kgp3074751      4.737534e-15
15      58723426        rs1077835       8.918459e-11
16      56686970        rs148916841     2.375065e-12
19      11187358        rs144826254     3.641029e-11
19      45373276        rs11879589      1.034183e-09


I want a one off output like
Code:
chr1 minValue  maxValue
chr2 minValue maxValue
chr10 minValue maxValue
chr15 minvalue maxValue
chr16 minValue maxValue
chr19 minValue maxValue

my chr1_GEN2bim looks like this
Code:
1       rs7514195       0       198000135       
1       rs6667378       0       198000253       
1       rs114753897     0       198000439

 

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set_color(1)                                                           fish                                                           set_color(1)

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