0
|
1 #!/bin/bash
|
|
2
|
|
3 inputfile=$1
|
|
4 col=$2
|
|
5 addremove=$3
|
|
6 outputfile=$4
|
|
7
|
|
8 echo "args: $@"
|
|
9 echo "inputfile: $inputfile"
|
|
10 echo "column: $column"
|
|
11 echo "addremove: $addremove"
|
|
12 echo "outputfile: $outputfile"
|
|
13
|
|
14 #get column number
|
|
15 column=`expr match "$col" '\([0-9]*\)'`
|
|
16 echo "colnumber: $column"
|
|
17
|
|
18 if [ $addremove == "add" ]
|
|
19 then
|
|
20 echo "adding prefix to column $column"
|
|
21 awk 'BEGIN{
|
|
22 FS="\t"
|
|
23 OFS="\t"
|
|
24 c="'"$column"'"
|
|
25 }{
|
|
26 if (index($0,"#")!=1){
|
|
27 $c="chr"$c
|
|
28 }
|
|
29 print $0
|
|
30
|
|
31 }END{}' $inputfile > $outputfile
|
|
32
|
|
33 else #remove prefix
|
|
34 echo "removing prefix from column $column"
|
|
35 awk 'BEGIN{
|
|
36 FS="\t"
|
|
37 OFS="\t"
|
|
38 c="'"$column"'"
|
|
39 }{
|
|
40 if (FNR>1 && index($0,"#")!=1){
|
|
41 $c=substr($c,4)
|
|
42 }
|
|
43 print $0
|
|
44
|
|
45 }END{}' $inputfile > $outputfile
|
|
46 fi
|
|
47
|
|
48 echo "inputfile: "
|
|
49 head -5 $inputfile
|
|
50
|
|
51 echo "outputfile: "
|
|
52 head -5 $outputfile
|