Question

Is it possible to use LC_ALL=C on a blast command?

1

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4.9 years ago

K.Gee ▴ 40

Hello. I am trying to run a blast against NR locally, and I am looking to find a way to run it as fast as I can. I recalled from my memory that I used LC_ALL=C fgrep -wf- for a "quicker" search file from one file to another, so I'm wondering if I can do something similar with the blast.

In the same line with fgrep I tried

blastp -query FILE -db LC_ALL=C /home/Protein_DataBases/nr/nr.fasta -evalue 1e-5 -outfmt 6 -num_threads 25 but it doesn't work. Does anyone knows if I can do this action??

Thank you in advance!

blast command • 1.3k views

ADD COMMENT • link 4.9 years ago by K.Gee ▴ 40

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You need to set locale outside of the programs you are trying to run. With blast your -db directive has to be followed by the blast index name. That setting is just going to force the programs to use default language for output.

ADD REPLY • link 4.9 years ago by GenoMax 147k

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Ok I see! Thank you very much for your response.

ADD REPLY • link 4.9 years ago by K.Gee ▴ 40

score 2 · Accepted Answer · 2020-01-10

Don't put LC_ALL=C as a parameter to blast! That won't work.

You can set LC_ALL=C before a command:

LC_ALL=FOO; echo $LC_ALL

prints:

FOO

it gets applied to all commands run in that shell.

The best recommendation would be to export the variable in bash (preferable upon initialization) so that it is always applied.

export LC_ALL=C

you may run into various problems otherwise when it comes to bioinformatics tools and processes. Specifically sorting will be byte-wise when is set to C and alphabetical otherwise.