/ 
bioperl-1.2.2
/ Bio::AlignIO::bl2seq

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');
$aln = $in->next_aln();

DESCRIPTION

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();

   Pass in -report_type flag when initializing the object to have this
   pass through to the Bio::Tools::BPbl2seq object.  See that object.

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://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/

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 _

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