[Bioperl-l] BLASTing BioSeq objects

[James Wasmuth]

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