[Bioperl-l] BLASTing BioSeq objects

[Shawn]

actually, $sio->next_seq is a handle that returns a Bio::Seq object.
so u can pass what it returns directly to blast.

my $fact = Bio::Tools::Run::StandAloneBlast->new('program'=>'blastn',
	                                        'database'=>"mydb",
		                               'outfile'=>'tmp/xxx');


my $stringfh = new IO::String($query_str);
my $sio = new Bio::SeqIO(-fh => $stringfh, -format => 'fasta');
$fact->blastall($sio->next_seq);



On Wed, 2002-12-11 at 01:08, James Wasmuth wrote:
> That would give me a SeqIO object, Blast requires a Bio::Seq object.  So 
> I would then need to convert $seq to a Bio::Seq object?  If so, this is 
> fine, and thanks.
> James
> 
> Shawn wrote:
> 
> >oh ok, misread you. Your original solution was almost there.
> > this works for me:
> >
> >use Bio::SeqIO;
> >use IO::String;
> >my $query_str = ">A\nACCCCCCC";

> >my $stringfh = new IO::String($query_str);
> >my $sio = new Bio::SeqIO(-fh => $stringfh, -format => 'fasta');
> >my $seq = $sio->next_seq;
> >
> >print $seq->seq;
> >
> >
> >shawn
> >
> >On Wed, 2002-12-11 at 00:38, James Wasmuth wrote:
> >  
> >
> >>>my $seq = new Bio::Seq(-seq=>$query_str,-id=>"blast_seq");
> >>>my $fact = Bio::Tools::Run::StandAloneBlast->new('program'=>'blastn',
> >>>	                                        'database'=>"mydb",
> >>>		                               'outfile'=>'tmp/xxx');
> >>>my $blast_report = $fact->blastall($seq);
> >>> 
> >>>
> >>>      
> >>>
> >>Unfortunately I've tried something along these lines.  The problem seems 
> >>to caused by the query sequence being in fasta format.  In the error log 
> >>I get a message...
> >>
> >>"MSG: Attempting to set the sequence to [>GLBH_CAEEL
> >><--some aa-->] which does not look healthy"
> >>
> >>I know that this is because entering a sequence using '-seq' it has to 
> >>be raw and so have no fasta header or "\n" characters, so I am trying to 
> >>get round this.  I've done it by storing the query sequence as a file 
> >>and using this to blast with but had been hoping to avoid this...
> >>
> >>James
> >>
> >>
> >>
> >>Shawn wrote:
> >>
> >>    
> >>
> >>>You probably want to do:
> >>>
> >>>
> >>>cheers,
> >>>
> >>>shawn
> >>>
> >>>On Tue, 2002-12-10 at 23:40, James Wasmuth wrote:
> >>> 
> >>>
> >>>      
> >>>
> >>>>Hi all,
> >>>>
> >>>>I'm trying to blast a sequence which is introduced to the program as a 
> >>>>string all implemented as a CGI userinterface.  The sequence is in fasta 
> >>>>format, though I hope to extend this to any.
> >>>>
> >>>>I thought I had been able to create a Bio::Seq object from the string, 
> >>>>which StandAloneBlast requires,  by doing...
> >>>>
> >>>>my $stringfh = new IO::String($query_str);
> >>>>my $bioSeq_obj = new Bio::Seq(-fh => $stringfh, -format => 'fasta');
> >>>>
> >>>>however a check on the length of the sequence in the object reveals it 
> >>>>to be zero in length.
> >>>>
> >>>>Anyone any ideas?  Should I first create a SeqIO object and convert this 
> >>>>to a Bio::Seq object and then BLAST.  If so, how is this conversion done?
> >>>>
> >>>>I'm sure the answers are in the archive but have been unable to locate 
> >>>>them...
> >>>>
> >>>>Many Thanks
> >>>>James
> >>>>
> >>>>_______________________________________________
> >>>>Bioperl-l mailing list
> >>>>Bioperl-l@bioperl.org
> >>>>http://bioperl.org/mailman/listinfo/bioperl-l
> >>>>
> >>>>   
> >>>>
> >>>>        
> >>>>
> >>> 
> >>>
> >>>      
> >>>
> >>-- 
> >>
> >>Nematode Bioinformatics
> >>Blaxter Nematode Genomics Group
> >>Institute of Cell, Animal and Population Biology
> >>Ashworth Labs
> >>University of Edinburgh
> >>King's Buildings
> >>Edinburgh
> >>EH9 3JT
> >>
> >>0131 650 7403
> >>
> >>
> >>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l@bioperl.org
> >>http://bioperl.org/mailman/listinfo/bioperl-l
> >>
> >>    
> >>
> >
> >
> >  
> >
> 
> -- 
> 
> Nematode Bioinformatics
> Blaxter Nematode Genomics Group
> Institute of Cell, Animal and Population Biology
> Ashworth Labs
> University of Edinburgh
> King's Buildings
> Edinburgh
> EH9 3JT
> 
> 0131 650 7403
> 
> 
>