Genome Annotation Output Files Naming
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14 months ago
Fid_o ▴ 20

I ran this annotation command: for k in *.fasta; do prokka $k --outdir "$k".prokka.output; echo $k; done on hundreds of assembled sequences. Each sequence annotation output produced a folder named "sequence_name.prokka.output" but the actual files in the folders were named according to the date e.g. "PROKKA_03062020.gff" for all the folders.

Now I want the actual output be named with the actual FASTA file ID. Example: sequence ID of D02502 should be like this: "PROKKA_D02502.gff"

What do I add (or remove) from the code above?

Annotation genome • 660 views
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14 months ago
Mensur Dlakic ★ 11k
for k in *.fasta; do prokka $k --outdir "$k".prokka.output --prefix PROKKA_$k; echo $k; done
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Thank you sooooo much Mensur Dlakic.

I am learning Bioinformatics and your help is great.

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Is there a way to put all prokka output from all fasta files in one folder rather than the traditional output (one folder for the output of each fasta)?

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