[Bioperl-l] Is it possible to parse BLAST output using IO:String?

Ryan Golhar golharam at umdnj.edu
Mon Oct 30 15:54:29 EST 2006


Thanks.  How are you getting the output?  system()?  BTW- I'm using
v1.5.1...




> -----Original Message-----
> From: Bernd Web [mailto:bernd.web at gmail.com] 
> Sent: Monday, October 30, 2006 3:45 PM
> To: golharam at umdnj.edu
> Cc: bioperl-l
> Subject: Re: [Bioperl-l] Is it possible to parse BLAST output 
> using IO:String?
> 
> 
> Hi Ryan,
> 
> I parse blastn output using IO::String w/o problems:
> 
>  my $stringfh = new IO::String($input);
>  my $in = new Bio::SearchIO(-format => 'blast', -fh => $stringfh);
> 
> however this is input does not come via backticks.
> 
> 
> bernd
> 
> On 10/30/06, Ryan Golhar <golharam at umdnj.edu> wrote:
> > I'm trying to parse some blast output w/o actually creating 
> the output 
> > file.  Instead, I'm capturing the output in a variable and 
> would like 
> > to use IO::String to represent the file:
> >
> >         $_ = `megablast -d somedatabase -i somesequence -D 2`;
> >         my $blast_file = new IO::String($_);
> >         my $searchio = new Bio::SearchIO(-format => 'blast', -fh => 
> > $blast_file);
> >         my $results = $searchio->next_result;
> >         my $hit = $results->next_hit;
> >         if (! defined($hit)) {
> >                 warn "No BLAST hit for $accession on chr $chr for 
> > Seq/$orth_id/$organism\n\n";
> >                 return;
> >         }
> >
> > Now, when Bio::SearchIO tries to read the output line by 
> line, instead 
> > it reads the entire output as 1 line.
> >
> > If I provide the output in a file and use:
> >
> >         my $searchio = new Bio::SearchIO(-format => 
> 'blast', -file => 
> > '/tmp/somefile.blast');
> >
> > This works...so is it possible to use IO::String to provide 
> > Bio::SearchIO with BLAST output?
> >
> > Ryan
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 



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