NAME

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

SYNOPSIS

       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();

DESCRIPTION

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

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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 the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Peter Schattner

       Email: schattner@alum.mit.edu

APPENDIX

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

   new
        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)

   next_aln
        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

   report_type
        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)