/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ 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",
                         -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://github.com/bioperl/bioperl-live/issues

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)