seqkit grep output unexpected results

[ZedekiahZhou]

The command 'echo -e ">seq\nACGTTGCA" | seqkit grep -s -i -p AA' should not output any sequence.

However, this command output these sequence in my computer.

$ echo -e ">seq\nACGTTGCA"  | seqkit grep -s -i -p AA
>seq
ACGTTGCA

$ echo -e ">seq\nTTTTTT"  | seqkit grep -s -i -p AA
>seq
TTTTTT

$ seqkit version
seqkit v2.9.0

Could someone help me explain the results?

[shenwei356]

Please add -P.

  2. When searching by sequences, it's partly matching, and both positive
     and negative strands are searched.
     Please switch on "-P/--only-positive-strand" if you would like to
     search only on the positive strand.

[ZedekiahZhou]

Thanks! It worked.

This command:

echo -e ">seq\nACGTTGCA" | seqkit grep -s -i -p AA

is an example in the manual, in the part "10. Circular genome".

Maybe the -P should be also added to the examples in the manual.

[shenwei356]

Ah, thanks!