Replace pattern in one column bash-CodePudding

I have multiple *csv file that cat like:

#sample,time,N
SPH-01-HG00186-1_R1_001,8.33386,93
SPH-01-HG00266-1_R1_001,7.41229,93
SPH-01-HG00274-1_R1_001,7.63903,93
SPH-01-HG00276-1_R1_001,7.94798,93
SPH-01-HG00403-1_R1_001,7.99299,93
SPH-01-HG00404-1_R1_001,8.38001,93

And I try to wrangle cated csv file to:

#sample,time,N
HG00186,8.33386,93
HG00266,7.41229,93
HG00274,7.63903,93
HG00276,7.94798,93
HG00403,7.99299,93
HG00404,8.38001,93

I did:

for i in $(ls *csv); do line=$(cat ${i} | grep -v "#" | cut -d'-' -f3); sed 's/*${line}*/${line}/g'; done

Yet no result showed up... Any advice of doing so? Thanks.

CodePudding user response：

Use this Perl one-liner:

perl -i -pe 's{.*?-.*?-(.*?)-.*?,}{$1,}' *.csv

The Perl one-liner uses these command line flags:
-e : Tells Perl to look for code in-line, instead of in a file.
-p : Loop over the input one line at a time, assigning it to $_ by default. Add print $_ after each loop iteration.
-i.bak : Edit input files in-place (overwrite the input file). Before overwriting, save a backup copy of the original file by appending to its name the extension .bak (you can omit .bak, to avoid creating any backup files).

CodePudding user response：

With awk:

awk -v FS=',' -v OFS=',' 'NR > 1 { split($1,w,"-"); $1 = w[3] } 1' file.csv

with sed:

sed -E 's/^([^-]*-){2}([^-]*)[^,]*/\2/' file.csv