cgeb2001's DokuWiki!

cut
-can split lines into chunks

1. can be based on columns or a delimiter

cut on columns

ENSTTRP00000013322 pep:novel scaffold:turTru1:scaffold_96599:113:67656:1 gene:ENSTTRG00000014049 transcript:ENSTTRT00000014049

ENSTTRP00000011169 pep:novel scaffold:turTru1:scaffold_95329:31817:82879:1 gene:ENSTTRG00000011774 transcript:ENSTTRT00000011776

ENSTTRP00000003887 pep:novel scaffold:turTru1:scaffold_112896:166326:170254:1 gene:ENSTTRG00000004129 transcript:ENSTTRT00000004129

cut -cfirst_number -second_number file

grep “>” tursiops.fa |cut -c1-19

ENSTTRP00000013322

ENSTTRP00000011169

ENSTTRP00000003887

grep “>” tursiops.fa |cut -c1-26

ENSTTRP00000013322 pep:no

ENSTTRP00000011169 pep:no

ENSTTRP00000003887 pep:no

cutting on columns works nicely if everything is lined up in neat columns
cut on delimiter
delimiter inside ““

1. default delimiter is a tab

grep ”>” tursiops.fa |cut -d“ ” -f1

ENSTTRP00000013322

ENSTTRP00000011169

ENSTTRP00000003887

grep “>” tursiops.fa |cut -d“ ” -f1-3

ENSTTRP00000013322 pep:novel scaffold:turTru1:scaffold_96599:113:67656:1

ENSTTRP00000011169 pep:novel scaffold:turTru1:scaffold_95329:31817:82879:1

ENSTTRP00000003887 pep:novel scaffold:turTru1:scaffold_112896:166326:170254:1

grep “>” tursiops.fa |cut -d“ ” -f3
scaffold:turTru1:scaffold_96599:113:67656:1
scaffold:turTru1:scaffold_95329:31817:82879:1
scaffold:turTru1:scaffold_112896:166326:170254:1

grep “>” tursiops.fa |cut -d“ ” -f3 |cut -d“:” -f3
scaffold_96599
scaffold_95329
scaffold_112896