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comparison column_extract.sh @ 0:e77c9484b2d0 draft default tip

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author saskia-hiltemann
date Thu, 22 Oct 2015 09:18:30 -0400
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-1:000000000000 0:e77c9484b2d0
1 #!/bin/bash
2
3 inputfile=$1
4 outputfile=$2
5 removeheader=$3
6 columns="$@"
7
8 cols="${columns// /,}" #make comma-separated
9
10 #skip first three arguments
11 firstcomma=`expr index "$cols" ,`
12 cols="${cols:$firstcomma}"
13 secondcomma=`expr index "$cols" ,`
14 cols="${cols:$secondcomma}"
15 thirdcomma=`expr index "$cols" ,`
16 cols="${cols:$thirdcomma}"
17 cols="${cols//:/}" #remove colons
18 echo "colums to print: $cols"
19
20 arr=$(echo $cols | tr "," "\n")
21
22 for x in $arr
23 do
24 echo $x
25 done
26
27 myArray=($columns)
28 i=3
29 len=${#myArray[@]}
30 mycols=""
31 echo "len: $len"
32 while [ $i -le $len ]
33 do
34 echo "myarray: ${myArray[$i]}"
35 mycols+=${myArray[$i]}
36 i=$[$i+2]
37 done
38 mycols="${mycols//:/,}" #make comma-separated
39 mycols="${mycols%?}"
40 echo "mycols: $mycols"
41
42 awk 'BEGIN{
43 FS="\t";
44 OFS="\t";
45 columns="'"$mycols"'";
46 len=split(columns,arr,",")
47 }{
48 if (index($1,"#")==1 || $1==""){ #print header as--s
49 if("'"$removeheader"'"=="N"){
50 print $0
51 }
52 }
53 else{
54 for (i=1;i<len;i++){
55 j=arr[i]
56 printf $j"\t"
57 }
58 j=arr[len]
59 printf $j"\n"
60 }
61 }END{
62
63 }' $inputfile > $outputfile
64
65