-task blastn option is not available in Bio::Tools::Run::StandAloneBlastPlus

[cjfields]

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Author Name: Peng Yu (Peng Yu) Original Redmine Issue: 3097, https://redmine.open-bio.org/issues/3097 Original Date: 2010-06-09 Original Assignee: Bioperl Guts

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Anyway, I restate my original problem below.

bioperl’s bl2seq by default is equivalent to the following command. blastn -query first.fa -subject second.fa

I want to add the option ‘-task blastn’. blastn -task blastn -query first.fa -subject second.fa

But I don’t find such option in bioperl’s bl2seq.

BTW, the bioperl code I used is listed below, where $seq1 and $seq2 are constructed from Bio::SeqIO->new.

my $factory = Bio::Tools::Run::StandAloneBlastPlus->new(); my $result=$factory->bl2seq( -method=>‘blastn’, -query=> $seq1, -subject=> $seq2 ); $factory->cleanup;