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();

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://bio.perl.org/MailList.html - About the mailing lists

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: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email: schattner@alum.mit.edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_aln
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

write_aln
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)