[Bioperl-l] low complexity filter in StandAloneBlastPlus

[Mark Jensen]

C., you might find http://bioperl.org/wiki/HOWTO:BlastPlus helpful, it has some more details than pod. There is a section "creating and using mask data". 

Cheers, MAJ


Sent from my T-Mobile 4G LTE Device

-------- Original message --------
From: Paul Cantalupo <pcantalupo at gmail.com> 
Date: 02/13/2014  5:48 PM  (GMT-05:00) 
To: Carnë Draug <carandraug+dev at gmail.com> 
Cc: "<bioperl-l at bioperl.org>" <bioperl-l at bioperl.org> 
Subject: Re: [Bioperl-l] low complexity filter in StandAloneBlastPlus 
 
Hi Carne,

Sorry for the confusion. Please check the documentation for each blast
program (blastn, blastp, etc...) on the command line with 'blastn -help'
and search for the section "Query filtering options". For example, this is
what I get for tblastn

$ tblastn -help | grep -A 10 'Query filtering'
*** Query filtering options
-seg <String>
   Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
   'no' to disable)
   Default = `12 2.2 2.5'
-soft_masking <Boolean>
   Apply filtering locations as soft masks
   Default = `false'
-lcase_masking
   Use lower case filtering in query and subject sequence(s)?

Depending on the blast flavor, you will either use -dust (for nucleotide
alignments) or -seg (for protein alignments). So, for tblastn, you need to
use -seg not -dust.

Take a look at line 28 of [2]. There you will see the usage of
-method_args. I just replaced -num_alignments with -dust in my previous
email. LMK if you have more questions...

Paul



Paul Cantalupo
University of Pittsburgh


On Thu, Feb 13, 2014 at 5:38 PM, Carnë Draug <carandraug+dev at gmail.com>wrote:

> On 13 February 2014 22:09, Paul Cantalupo <pcantalupo at gmail.com> wrote:
> > Hi Carne,
> >
> > Take a look at the synopsis of
> > Bio::Tools::Run::StandAloneBlastPlus::BlastMethods. I think you need to
> use
> > the method_args parameter:
> >
> >  $result = $fac->blastn( -query => 'query_seqs.fas',
> >                          -outfile => 'query.bls',
> >                          -method_args => [ '-dust' => 'no' ] );
> >
>
> Hi Paul
>
> thank for your reply but where do you see this documentation? This is
> neither in the last release [1], the bioperl-run repository [2], or
> the bioperl-live [3] (which doesn't even have ::BlastMethods).
>
> Also, I did what you say but get a "Blast run: parameter 'dust' is not
> available for method 'tblastn'" error.
>
> This is my simple code, from the very start (including creation of the
> database):
>
> Bio::Tools::Run::StandAloneBlastPlus->new(
>   -db_data => $db_data,
>   -db_name => $db_name,
>   -create => 1,
> )->make_db();
>
> my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
>   -db_name => $db_name,
> );
>
> foreach my $file (@files) {
>   my $result = $fac->tblastn(
>     -query   => $file,
>     -outfile => $file . '.bls',
>     -method_args => ['-dust' => 'no'],
>   );
>   ## do stuff with $result
> }
>
> Thank you
> Carnë
>
> [1]
> https://metacpan.org/pod/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods
> [2]
> https://github.com/bioperl/bioperl-run/blob/master/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
> [3]
> https://github.com/bioperl/bioperl-live/blob/master/Bio/Tools/Run/StandAloneBlast.pm
>

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