[Biopython] Running a specific version of NCBI BLAST from within Biopython

[Ivan Gregoretti]

Thank you Jocelyne and Peter.

Knowing that the first argument to these APIs is the binary path
solves my problem.

Thank you.

Ivan




Ivan Gregoretti, PhD
Bioinformatics



On Mon, Oct 20, 2014 at 5:48 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Mon, Oct 20, 2014 at 8:08 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
>> Hello Biopythoneers,
>>
>> I have multiple versions of NCBI BLAST installed in my Linux box. I
>> need them all.
>>
>> How do I tell Biopython which version of local BLAST I want to run each time?
>>
>> Is it possible to specify the path to the desired executable?
>>
>> Thank you,
>>
>> Ivan
>
> Yes - assuming you are using the command line wrappers to build
> the command string (and run it), they default to calling blastp or
> blastx (etc) meaning the first binary of that name on the $PATH.
> However, you can provide the explicit path to the binary you want.
>
> i.e.
>
> from Bio.Blast.Applications import NcbiblastxCommandline
> blastx_cline = NcbiblastxCommandline(query="opuntia.fasta", db="nr",
> evalue=0.001, outfmt=5, out="opuntia.xml")
>
> is equivalent to giving the first argument (cmd) explicitly:
>
> from Bio.Blast.Applications import NcbiblastxCommandline
> blastx_cline = NcbiblastxCommandline("blastx", query="opuntia.fasta",
> db="nr", evalue=0.001, outfmt=5, out="opuntia.xml")
>
> which you can change to something like:
>
> from Bio.Blast.Applications import NcbiblastxCommandline
> blastx_cline = NcbiblastxCommandline("/mnt/shared/ncbi-blast-2.2.29+/blastx",
> query="opuntia.fasta", db="nr", evalue=0.001, outfmt=5,
> out="opuntia.xml")
>
> In all our command line wrappers using this style API, the first
> argument is the binary name.
>
> Peter
>
> P.S. On Windows the $PATH is often not set, so you are forced to
> give the full path of the BLAST+ binaries like this.