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bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
GNU General Public License v3.0
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output both daa and outfmt 6 in the same run? #665

Open khoojj opened 1 year ago

khoojj commented 1 year ago

Hi! I wonder if there is a way to output daa (for MEGAN) and outfmt6 at the same time?

I will also need the taxonomy info (ie. staxids | sskingdoms | skingdoms | sphylums | sscinames | stitle) in the outfmt 6 out file - I suppose these are not stored in the daa format.

What is the best way to obtain both formats without having to run the alignment twice?

Suggestion will be appreciated!

Thanks!

bbuchfink commented 1 year ago

There is no other way than running the alignment twice. The DAA format is deprecated and will not be developed further. Of course it is possible to take the diamond tabular output and join it against the accession to taxid mapping manually using a database system or standard shell commands.

bbuchfink commented 1 year ago

To be more precise: I meant using diamond view to convert the DAA to tsv, then joining against the taxonomy mapping.

khoojj commented 1 year ago

Alright thanks!

On Thu, Feb 16, 2023, 11:37 AM Benjamin Buchfink @.***> wrote:

To be more precise: I meant using diamond view to convert the DAA to tsv, then joining against the taxonomy mapping.

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