Enhancement to to pass a pre-built BLAST db to dnabarcoder search

[aringeri]

Hello,

I have a situation where I am calling dnabarcoder.py search multiple times with different query datasets but the reference database stays the same.
Each time I execute the search function, there is a bit of a delay to complete the makeblastdb command.

Would it be possible to add an argument to dnabarcoder's search command which takes a pre-built BLAST database so it doesn't need to be recomputed each time?

Thank you

[vuthuyduong]

Dear Alex, Thank you for your suggestion. I've modified the classification/search.py file, so that we only need to run the makeblastdb command for the first time. The pre-built BLAST database files are saved in the output folder of dnabarcoder. If you wish to remake these files, please delete the existing files. Cheers

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On Thu, 12 Sept 2024 at 07:38, Alex Ringeri ***@***.***> wrote: Hello, I have a situation where I am calling dnabarcoder.py search multiple times with different query datasets but the reference database stays the same. Each time I execute the search function, there is a bit of a delay to complete the makeblastdb command. Would it be possible to add an argument to dnabarcoder's search command which takes a pre-built BLAST database so it doesn't need to be recomputed each time? Thank you — Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF6CZMRQYY72FDE7KBIRQVTZWESGDAVCNFSM6AAAAABOCMA6EWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZDCMZZGU3DAOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[aringeri]

Hi Duong,

Thank you very much for your update and quick turnaround!
I believe I can make this work with my pipeline.

Alex