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vuthuyduong / dnabarcoder

Apache License 2.0
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Enhancement to to pass a pre-built BLAST db to dnabarcoder search #3

Open aringeri opened 1 month ago

aringeri commented 1 month ago

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 commented 1 month ago

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

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 https://github.com/vuthuyduong/dnabarcoder/issues/3, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF6CZMRQYY72FDE7KBIRQVTZWESGDAVCNFSM6AAAAABOCMA6EWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZDCMZZGU3DAOI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

aringeri commented 1 month ago

Hi Duong,

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

Alex