Question: Adding -type arguments of blastn in Bioperl
0
gravatar for adhirajnath14
9 months ago by
adhirajnath1430 wrote:

I need to run a blast for small query sequence in bioperl. The way to do it in blast standalone program is by adding

./blastn -db nt -remote -query test2.seq -task "blastn-short" -out test2.out

Is there a way to add -task arguments in BioPerl?

Thank you

sequence alignment • 208 views
ADD COMMENTlink modified 9 months ago by JC10k • written 9 months ago by adhirajnath1430
0
gravatar for JC
9 months ago by
JC10k
Mexico
JC10k wrote:

Check https://bioperl.org/howtos/BlastPlus_HOWTO.html

ADD COMMENTlink written 9 months ago by JC10k

Thank you sir for responding. I tried $result = $fac->blastn( -query => 'myquery.fasta', -task -> 'blastn-short' -outfile => 'result01.txt', -outformat => 9)

It does not work.

ADD REPLYlink written 9 months ago by adhirajnath1430

in case you copy/pasted this there's a typo after -task -> must be =>:

$result = $fac->blastn( -query => 'myquery.fasta', -task -> 'blastn-short' -outfile => 'result01.txt', -outformat => 9)
                                                         /\
ADD REPLYlink modified 9 months ago • written 9 months ago by Carambakaracho2.2k

Sorry about the typo. I didn't copy paste it, that's why. Anyway, it does not work with it.

ADD REPLYlink written 9 months ago by adhirajnath1430
1

from a short glimpse it seems that either you have to call it via blastn-short or specify task using method_args:

$result = $fac->blastn-short( -query => 'myquery.fasta', -outfile => 'result01.txt', -outformat => 9)

$result = $fac->blastn( -query => 'query_seqs.fas',
                    -outfile => 'query.bls',
                    -method_args => [ -task => "blastn-short"
                                      -num_alignments => 10,
                                      -evalue => 100 ]);

Bear in mind I'm only guessing

ADD REPLYlink modified 9 months ago • written 9 months ago by Carambakaracho2.2k

Thank you so much. It worked!

ADD REPLYlink written 9 months ago by adhirajnath1430
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