Bio::AlignIO::bl2seq(3pm) User Contributed Perl Documentation Bio::AlignIO::bl2seq(3pm)
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)
perl v5.14.2 2012-03-02 Bio::AlignIO::bl2seq(3pm)