Provided by: libbio-perl-perl_1.7.2-2_all bug


       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",
                                    -report_type => "blastn");
           $aln = $in->next_aln();


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

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

          # Get two 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);
          # Note that report is a Bio::SearchIO object

          # Use 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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AUTHOR - Peter Schattner



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

        Title   : new
        Usage   : my $alignio = Bio::SimpleAlign->new(-format => 'bl2seq',
                                                      -file   => 'filename',
                                                      -report_type => 'blastx');
        Function: Get a L<Bio::SimpleAlign>
        Returns : L<Bio::SimpleAlign> object
        Args    : -report_type => report type (blastn,blastx,tblastx,tblastn,blastp)

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

   write_aln (NOT IMPLEMENTED)
        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

        Title   : report_type
        Usage   : $obj->report_type($newval)
        Function: Sets the report type (blastn, blastp...)
        Returns : value of report_type (a scalar)
        Args    : on set, new value (a scalar or undef, optional)