How to replace the "." in a table with "0"
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0
Entering edit mode
4.4 years ago
bright602 ▴ 50

Hi there, I am working with a gff file, however I find that the 8th phase column of CDS are "." instead of integers such as "0" or "1" or "2". Could anyone show me a command line that can replace the "." with "0" in 8th column when the 4th column is CDS?

Thanks!

DDB0232428  Sequencing Center   exon    1890    3287    .   +   .   Parent=DDB0216437
DDB0232428  Sequencing Center   CDS 1890    3287    .   +   .   Parent=DDB0216437
DDB0232428  Sequencing Center   exon    3848    4855    .   +   .   Parent=DDB0216438
DDB0232428  Sequencing Center   CDS 3848    4855    .   +   .   Parent=DDB0216438

next-gen sequence • 712 views
3
Entering edit mode
4.4 years ago
ATpoint 62k
awk 'OFS="\t" {if ($4 == "CDS")$8 = "0"; print \$0}' in.gff > out.gff