seqret: command not found

Question

[ÖZGÜN]

Hello,

I'm using macMonterey 12.6

I try to convert GenBank file into GFF3 or FASTA but when I scripted to code ""cat AF086833.gb | seqret -filter -feature -osformat gff3 > AF086833.gff", the shell gives an error "zsh: command not found: seqret". How can I solve it and should I bash instead of zsh?

[rpolicastro]

Is seqret installed? which seqret

[ÖZGÜN]

no, I didn't install. How can I install?

Answer 1

[Istvan Albert]

you need to install the seqretbut that's a not so easy task you need conda etc.

what is more problematic, though, is that the GFF conversion via seqret is not that great either, I forgot the exact details, but there are inconsistencies

it is best if you get the gff directly; you could use a tool I wrote bio

pip install bio --upgrade

then you can do:

bio fetch AF086833 --format gff > AF086833.gff

or

 cat AF086833.gb  | bio gff > AF086833.gff

the two GFF files will not be identical, as the first obtains the GFF file from NCBI whereas the latter converts the GenBank to GFF.

The GFF distributed by NCBI may contain information that is not present in the GenBank file

[ÖZGÜN]

thank you for explanation, I have conda so I installed easily.