[Bioperl-l] BioPerl Parsing problems

Jason Stajich jason.stajich at duke.edu
Tue Dec 28 13:06:51 EST 2004

I think you want $hsp->significance() for BPlite - if you follow the 
inheritance hierarchy you'll see that BPlite::HSP is-a 
SeqFeature::SimilarityPair which is-a SeaFeature::Similarity which has 
the significance method.

On Dec 28, 2004, at 11:59 AM, David García Cortés wrote:

> Hello.
> I'm trying to parse the results of a blast query, using BPLite. The 
> problem is: I can't access the evalue of a HSP. For accessing the 
> score, there are no problems: I only have to access the HSP's field 
> "score. But... what with evalue? If I do the same using "evalue", 
> there's an error: it can't find that field on the HSP.
> Here you can see the main part of the code:
> $factory = Bio::Tools::Run::StandAloneBlast->new(@pars);
> my $blst_rprt = $factory->blastall($seq);
> my $exists_results = parse_blast($blst_rprt);
> And the function parse_blast is this:
> sub parse_blast {
> my $blast_report = shift;
>  while (my $result = $blast_report->nextSbjct) {
>    while ( my $hsp = $result->nextHSP )
>    {
>    my $score    = $hsp->score;
>    my $evalue    = $hsp->evalue;
>    }
>  }
> }
> A different problem (although closely related with the one above) i'd 
> like to ask is this:
> I thought that maybe it'd be better to use SearchIO for the parsing, 
> but then the problem is that when creating a SearchIO variable, you 
> have to pass the name of the file where the blast result to parse is. 
> But as you can see in the code, my blast result is in the variable 
> $blst_rprt (or $blast_report), not in a file. So should I write the 
> content of the $blast_report variable into a file, and pass this file 
> to SearchIO? I don't like this solution; i would be grateful if you 
> could give me an alternative one.
This is something you can ask StandAloneBlast to do for you by return a 
Bio::SearchIO object provide the option
_READMETHOD => 'Blast' in @params array that you using.

This should be the default in recent releases of Bioperl (i.e. you can 
only get BPlite object if you specify _READMETHOD => 'BPlite') so it 
would depend on what version of Bioperl you are using.

You can also save the blast report to a file if you provide the -o => 
'filename' option in @params to write the report to a file and can then 
reopen it with Bio::SearchIO.


> Thank you in advance.
> --
> David García Cortés
> Instituto Nacional de Bioinformática (INB)
> Nodo Computacional GNHC-2 UPC-CIRI
> c/. Jordi Girona 1-3
> Modul C6-E201                   Tel.  : 934 011 650
> E-08034 Barcelona              Fax   : 934 017 014
> Catalunya (Spain)                e-mail: davidg at lsi.upc.edu
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Jason Stajich
jason.stajich at duke.edu

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