Fw: [Bioperl-l] PBbl2seq Object

[Jason Stajich]

----- Original Message -----
From: "Jason Stajich" <jason@chg.mc.duke.edu>
To: <holger@tupath.de>; <'bioperl-l@bioperl.org'>
Sent: Monday, July 16, 2001 10:25 AM
Subject: Re: [Bioperl-l] PBbl2seq Object


> Is this 2 separate reports concatenated together or just multiple
alignments
> for the same report?
>
> There is a reported bug (jitterbug #940) to handle multiple alignments in
> the same report.  We have fixed on the main trunk but the fix is not in
the
> 0.7 branch because it required an interface change.
> http://bio.perl.org/bioperl-bugs/Fixed-Bugs?id=940
>
> If you are running off bioperl-live main trunk code this may need to be a
> new bug submission as I don't see anything like this in the queue.
>
> In the meantime you'll probably want to write a little script that
> preprocesses the bl2seq data and creates a separate file/filehandle for
each
> report.  Can show you how to do that if you aren't sure what to do.
>
> This will be something that I'll be sure and bring up at BOSC to see if we
> are handling correctly.
>
> -Jason
>
> ----- Original Message -----
> From: "Holger Tupath" <holger@tupath.de>
> To: <'bioperl-l@bioperl.org'>; <ioperl-l@bioperl.org>
> Sent: Friday, July 13, 2001 6:13 AM
> Subject: [Bioperl-l] PBbl2seq Object
>
>
> > Hi,
> > I want to use the PBbl2seq Object to parse an output file from bl2seq.
> > The module works fine for the first entry in the output file, but how do
I
> > get the data for the next entry ?
> >
> > Does anybody have an example script ?
> >
> >
> >
> >
> > This code snippet prints all the data in the object, after creation from
> the
> > output file. (prints the first entry in the file)
> >
> > #!/usr/bin/perl
> >
> > use Bio::Tools::BPbl2seq;
> > my $report = Bio::Tools::BPbl2seq->new(-file => 'blast_output');
> >
> >
> > print "match() -> ".$report->match()."\n";
> > print "P() -> ".$report->P()."\n";
> > print "percent() -> ".$report->percent()."\n";
> > print "positive() -> ".$report->positive()."\n";
> > print "score() -> ".$report->score()."\n";
> > print "bits() -> ".$report->bits()."\n";
> > print "query() -> ".$report->query()."\n";
> >
> > print "querySeq() -> ".$report->querySeq()."\n";
> > print "sbjctSeq() -> ".$report->sbjctSeq()."\n";
> > print "homologySeq() -> ".$report->homologySeq()."\n";
> >
> > print "qs() -> ".$report->qs()."\n";
> > print "ss() -> ".$report->ss()."\n";
> > print "hs() -> ".$report->hs()."\n";
> >
> >
> > thanx !
> >
> >
> > Holger
> >
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
>