Hi everyone,
I have a dataset of fasta file which looks like this:
>13_seq2344_ATCGACGGAACTGA
>1342_seq2134_AGCTGTGGCAT
>130_SEQ2289_TCGAATCGAGGAAC
I want to remove the line which contains "13" only
so my output should look like:
>1342_seq2134_AGCTGTGGCAT
>130_SEQ2289_TCGAATCGAGGAAC
I am trying grep -w, grep -o, grep -E all these are not working for me.
Do suggest any command that works.
Thank you
•
written
by
Confused_human •
Hi!
awk '!/^13_/' file.fa > new_file.fa
Should remove the line beginning with 13 only. The substring inbetween the slashes is what is searched for so you could play with this if you need to. The ! is a logical for NOT which means print these lines if they do NOT contain the pattern.
Hope this helps :)
EDIT - See below!
Should remove the line beginning with 13 only
No.
$ cat test.txt
>13_seq2344_ATCGACGGAACTGA
>1342_seq2134_AGCTGTGGCAT
>130_SEQ2289_TCGAATCGAGGAAC
>113_test
$ awk '!/13_/' test.txt
>1342_seq2134_AGCTGTGGCAT
>130_SEQ2289_TCGAATCGAGGAAC
$ awk '!/^>13_/' test.txt
>1342_seq2134_AGCTGTGGCAT
>130_SEQ2289_TCGAATCGAGGAAC
>113_test
Log in to answer this question.
or
you also have to think about removing sequences as well. Try this:
seqkit -w 0 grep -vrip "^13_" input.fa. Awk or sed remove only the matching the line, not the following sequences. It is difficult if sequences are in multlines.