Ewan Birney


Bio::AlignIO::bl2seq - bl2seq sequence input/output stream


Do not use this module directly. Use it via the Bio::AlignIO class, as in:

    use Bio::AlignIO;

    $in  = Bio::AlignIO->new(-file => "inputfilename" , '-format' => 'bl2seq');
    $aln = $in->next_aln();


This object can create Bio::SimpleAlign sequence alignment objects (of 2 sequences) from bl2seq BLAST reports.

A nice feature of this module is that- in combination with StandAloneBlast.pm or remote blasting - it can be used to align 2 sequences and make a SimpleAlign object from them which can then be manipulated using any SimpleAlign.pm methods, eg:

   #Get 2 sequences
   $str = Bio::SeqIO->new(-file=>'t/amino.fa' , '-format' => 'Fasta', );
   my $seq3 = $str->next_seq();
   my $seq4 = $str->next_seq();

   # Run bl2seq on them
   $factory = Bio::Tools::StandAloneBlast->new('program' => 'blastp', 
                                               'outfile' => 'bl2seq.out');
   my $bl2seq_report = $factory->bl2seq($seq3, $seq4);

   # Use AlignIO.pm to create a SimpleAlign object from the bl2seq report
   $str = Bio::AlignIO->new(-file=> 'bl2seq.out','-format' => 'bl2seq');
   $aln = $str->next_aln();


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  bioperl-l@bioperl.org               - General discussion
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Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:


AUTHOR - Peter Schattner

Email: schattner@alum.mit.edu


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
            or on error
 Args    : NONE


 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in bl2seq format
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object