Bio::Prospect::Align -- Package for overlaying multiple Prospect alignments
$Id: Align.pm,v 1.15 2003/11/18 19:45:45 rkh Exp $
use Bio::Prospect::Options; use Bio::Prospect::LocalClient; use Bio::Prospect::Align; use Bio::SeqIO; my $in = new Bio::SeqIO( -format=> 'Fasta', '-file' => $ARGV[0] ); my $po = new Bio::Prospect::Options( seq=>1, svm=>1, global_local=>1, templates=>[qw(1bgc 1alu 1rcb 1eera)] ); my $pf = new Bio::Prospect::LocalClient( {options=>$po} ); while ( my $s = $in->next_seq() ) { my @threads = $pf->thread( $s ); my $pa = new Bio::Prospect::Align( -debug=>0,-threads => \@threads ); print $pa->getAlignment(-format=>'html'); }
Bio::Prospect::Align represents an alignment of one or more Prospect structural alignments.
Name: new() Purpose: return Bio::Prospect::Align object Arguments: -threads => [ Bio::Prospect::Thread objects ], Returns: Bio::Prospect::Align object
Name: get_alignment() Purpose: return the sequence alignment of the Bio::Prospect::Thread objects Arguments: -format => one of: 'clustalw', 'bl2seq','clustalw', 'emboss','fasta','mase','mega','meme','msf','nexus', 'pfam','phylip','prodom','psi','selex','stockholm' (default: clustalw) -show_ss => output secondard structure (default: off) -show_seq => output target sequence (default: on) Returns: scalar containing the alignment
Name: get_threads() Purpose: return the Bio::Prospect::Thread object list associated with this object Arguments: none Returns: list of Bio::Prospect::Thread objects
The following functions are documented for developers' benefit. THESE SHOULD NOT BE CALLED OUTSIDE OF THIS MODULE. YOU'VE BEEN WARNED.
Name: _align() Purpose: private method that does the alignment work - called by new(). Builds a clustalw alignment internally. use get_alignment() to retrieve the alignment in other formats. Arguments: -show_ss => 0 | 1 output secondard structure (default: off) -show_seq => 0 | 1 output target sequence (default: on) Returns: nothing
@@banner@@
To install Bio::Prospect::File, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Prospect::File
CPAN shell
perl -MCPAN -e shell install Bio::Prospect::File
For more information on module installation, please visit the detailed CPAN module installation guide.