[Bioperl-l] parsing blast output

[Will Spooner]

Hi Jason,

I have, in the past, wanted to work with HSP objects out of context of the 
Hit object. There is currently no way to fetch the description in this 
case. How easy would it be to propogate the $hit->description to the 
$hsp->seqdesc attribute during the report parsing?

Will

On Sat, 18 Jun 2005, Jason Stajich wrote:

> Except that hits() returns a list.
> while( my $result = $blast_report->next_result ) {
>   while( my $hit= $result->next_hit ) {
>    print $hit->name, " ", $hit->description, "\n";
>   }
> }
> 
> See the HOWTO as well.
> 
> On Jun 18, 2005, at 6:41 AM, Irshad Khan wrote:
> 
> > On 6/18/05, Irshad Khan <iak13000 at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> If it is in the description part may be you can try this
> >>
> >> $blast_report->next_result->hits()->description;
> >>
> >> let me know if it works
> >>
> >> Irshad
> >>
> >> On 6/18/05, Tuan A. Tran <tuantran167 at gmail.com> wrote:
> >>
> >>> Hi,
> >>>
> >>> When I blasted my query sequence against a database, the got the
> >>> following line (for example)
> >>>
> >>>
> >>>> 3R type=chromosome; loc=3R:1..27905053; ID=3R; release=r4.1;  
> >>>> species=dmel
> >>>>
> >>>
> >>> Using bioperl module,
> >>>  $blast_report = $factory->blastall($query);
> >>> I can extract some information like ID = 3R using
> >>>  $blast_report->next_result->hits()->name;
> >>>
> >>>  If I want to keep the entire line as show above what should I  
> >>> do? Is
> >>> there a module in bioperl? I really appreciate if someone can  
> >>> tell me
> >>> how to do it.
> >>>
> >>> Thanks,
> >>> TAT
> >>>
> >>> _______________________________________________
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> >>> Bioperl-l at portal.open-bio.org
> >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>
> >>
> >
> > _______________________________________________
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> >
> 
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12/
> 
> 
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