[Bioperl-l] And the correct answer is...

[Dominique Vlieghe]

Hello all,

Thanks for your swift replies:  the correct way to do this is

use Bio::Tools::BPbl2seq;
my $report = *Bio::Tools::BPbl2seq*->new(-file => 'bl2seq.out', 
-report_type => 'blastn');

while(my $hsp = $report->next_feature) {
print
$hsp->query->strand."\n".
$hsp->sbjct->strand."\n";
}

(quite simple, in retrospect)

cheerz

D

Brian Osborne wrote:

>Dominique,
>
>I think this is discussed in the FAQ,
>http://bioperl.org/Core/Latest/faq.html#Q3.5, and in the SearchIO HOW TO.
>
>Brian O.
>
>-----Original Message-----
>From: bioperl-l-bounces at portal.open-bio.org
>[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Dominique Vlieghe
>Sent: Monday, March 29, 2004 7:21 AM
>To: bioperl-l at portal.open-bio.org
>Subject: [Bioperl-l] "strand" line in bl2seq output
>
>Hello all,
>
>I have a question regarding the parsing of bl2seq output (using
>Bio::Tools::BPbl2seq). In the bl2seq output there is a line for strand
>orientation (e.g. "Strand = Plus / Plus"). I looked at the modules that
>parse this file, but I don't see where those lines are processed. Is
>this correct? If it is, what's the alternative for getting this valuable
>information?
>
>Regards
>
>Dominique
>
>--
>-----------------------------
>Save the Hubble petition: http://www.savethehubble.org
>------------------------------
>Dominique Vlieghe, Ph.D.,
>Bioinformatics Core,
>Department for Molecular Biomedical Research (DMBR)
>VIB - Ghent University
>'Fiers-Schell-Van Montagu' building
>Technologiepark 927
>B-9052 Ghent (Zwijnaarde), Belgium
>
>Tel : +32-(0)9-33-13.693
>Fax : +32-(0)9-33-13.609
>email:dominique.vlieghe at dmbr.ugent.be
>www:http://www.dmbr.ugent.be/
>------------------------------
>
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>
>
>  
>


-- 
-----------------------------
Save the Hubble petition: http://www.savethehubble.org
------------------------------
Dominique Vlieghe, Ph.D.,
Bioinformatics Core,
Department for Molecular Biomedical Research (DMBR)
VIB - Ghent University
'Fiers-Schell-Van Montagu' building
Technologiepark 927
B-9052 Ghent (Zwijnaarde), Belgium

Tel : +32-(0)9-33-13.693
Fax : +32-(0)9-33-13.609
email:dominique.vlieghe at dmbr.ugent.be
www:http://www.dmbr.ugent.be/
------------------------------