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Consider:

seqkit grep -nrp ";s__nosocomialis;" ribogrove_11.217_sequences.fasta

Using this command lets me select all sequences related to the organism "A. nosocomialis" in the RiboGrove database.

How do I save these selected sequences to a new ".fasta" file?

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2 Answers 2

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Based on the docs, seqkit grep has a -o "output file" option, so if you get the correct output with:

seqkit grep -nrp ";s__nosocomialis;" ribogrove_11.217_sequences.fasta

Then this command will (in theory) give you your desired outcome:

seqkit grep -nrp ";s__nosocomialis;" ribogrove_11.217_sequences.fasta -o new.fasta
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    $\begingroup$ Thanks, it worked. I don't know how i didn't see the output command while surfing the documentation. $\endgroup$
    – Freezing Soul
    Apr 22 at 6:19
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For any program that prints output to the terminal (standard output), you can always redirect to a file using > or >>. Either of the two will create the output file if it doesn't exist, but > will overwrite any contents of an already existing file, while >> will append to it without overwriting. So you could just do:

seqkit grep -nrp ";s__nosocomialis;" ribogrove_11.217_sequences.fasta > out.fa
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