#
# BioPerl module for Bio::Search::Tiling::TilingI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Mark A. Jensen <maj@fortinbras.us>
#
# Copyright Mark A. Jensen
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module
=head1 SYNOPSIS
Not used directly. Useful POD here for developers, however.
The interface is desgined to make the following code conversion as
simple as possible:
From:
# Bio::Search::SearchUtils-based
while ( local $_ = $result->next_hit ) {
printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n",
$hit->significance, $hit->frac_aligned_query, $hit->num_identical);
}
To:
# TilingI-based
while ( local $_ = $result->next_hit ) {
my $tiling = Bio::Search::Tiling::MyTiling($_);
printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n",
$hit->significance, $tiling->frac_aligned_query, $tiling->num_identical);
}
=head1 DESCRIPTION
This module provides strong suggestions for any intended HSP tiling
object implementation. An object subclassing TilingI should override
the methods defined here according to their descriptions below.
See the section STATISTICS METHODS for hints on implementing methods
that are valid across different algorithms and report types.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Mark A. Jensen
Email maj@fortinbras.us
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Search::Tiling::TilingI;
use strict;
use warnings;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use base qw(Bio::Root::Root);
=head2 STATISTICS METHODS
The tiling statistics can be thought of as global counterparts to
similar statistics defined for the individual HSPs. We therefore
prescribe definitions for many of the synonymous methods defined in
L<Bio::Search::HSP::HSPI>.
The tiling statistics must be able to keep track of the coordinate
systems in which both the query and subject sequences exist; i.e.,
either nucleotide or amino acid. This information is typically
inferred from the name of the algorithm used to perform the original
search (contained in C<$hit_object-E<gt>algorithm>). Here is a table
of algorithm information that may be useful (if you trust us).
algorithm query on hit coordinates(q/h)
--------- ------------ ---------------
blastn dna on dna dna/dna
blastp aa on aa aa/aa
blastx xna on aa dna/aa
tblastn aa on xna aa/dna
tblastx xna on xna dna/dna
fasta dna on dna dna/dna
fasta aa on aa aa/aa
fastx xna on aa dna/aa
fasty xna on aa dna/aa
tfasta aa on xna aa/dna
tfasty aa on xna aa/dna
megablast dna on dna dna/dna
xna: translated nucleotide data
Statistics methods must also be aware of differences in reporting
among the algorithms. Hit attributes are not necessarily normalized
over all algorithms. Devs, please feel free to add examples to the
list below.
=over
=item NCBI BLAST vs WU-BLAST (AB-BLAST) lengths
The total length of the alignment is reported differently between these two flavors. C<$hit_object-E<gt>length()> will contain the number in the denominator of the stats line; i.e., 120 in
Identical = 34/120 Positives = 67/120
NCBI BLAST uses the total length of the query sequence as input by the user (a.k.a. "with gaps"). WU-BLAST uses the length of the query sequence actually aligned by the algorithm (a.k.a. "without gaps").
=back
Finally, developers should remember that sequence data may or may not
be associated with the HSPs contained in the hit object. This will
typically depend on whether a full report (e.g, C<blastall -m0>) or a
summary (e.g., C<blastall -m8>) was parsed. Statistics methods that
depend directly on the sequence data will need to check that
that data is present.
=head2 identities
Title : identities
Alias : num_identical
Usage : $num_identities = $tiling->identities()
Function: Return the estimated or exact number of identities in the
tiling, accounting for overlapping HSPs
Example :
Returns : number of identical residue pairs
Args :
=cut
sub identities{
my ($self,@args) = @_;
$self->throw_not_implemented;
}
#HSPI synonym
sub num_identical { shift->identities( @_ ) }
=head2 conserved
Title : conserved
Alias : num_conserved
Usage : $num_conserved = $tiling->conserved()
Function: Return the estimated or exact number of conserved sites in the
tiling, accounting for overlapping HSPs
Example :
Returns : number of conserved residue pairs
Args :
=cut
sub conserved{
my ($self,@args) = @_;
$self->throw_not_implemented;
}
#HSPI synonym
sub num_conserved { shift->conserved( @_ ) }
=head2 length
Title : length
Usage : $max_length = $tiling->length($type)
Function: Return the total number of residues of the subject or query
sequence covered by the tiling
Returns : number of "logical" residues covered
Args : scalar $type, one of 'hit', 'subject', 'query'
=cut
sub length{
my ($self, $type, @args) = @_;
$self->throw_not_implemented;
}
=head2 frac_identical
Title : frac_identical
Usage : $tiling->frac_identical($type)
Function: Return the fraction of sequence length consisting
of identical pairs
Returns : scalar float
Args : scalar $type, one of 'hit', 'subject', 'query'
Note : This method must take account of the $type coordinate
system and the length reporting method (see STATISTICS
METHODS above)
=cut
sub frac_identical {
my ($self, $type, @args) = @_;
$self->throw_not_implemented;
}
=head2 percent_identity
Title : percent_identity
Usage : $tiling->percent_identity($type)
Function: Return the fraction of sequence length consisting
of identical pairs as a percentage
Returns : scalar float
Args : scalar $type, one of 'hit', 'subject', 'query'
=cut
sub percent_identity {
my ($self, $type, @args) = @_;
return $self->frac_identical($type, @args) * 100;
}
=head2 frac_conserved
Title : frac_conserved
Usage : $tiling->frac_conserved($type)
Function: Return the fraction of sequence length consisting
of conserved pairs
Returns : scalar float
Args : scalar $type, one of 'hit', 'subject', 'query'
Note : This method must take account of the $type coordinate
system and the length reporting method (see STATISTICS
METHODS above)
=cut
sub frac_conserved{
my ($self, $type, @args) = @_;
$self->throw_not_implemented;
}
=head2 percent_conserved
Title : percent_conserved
Usage : $tiling->percent_conserved($type)
Function: Return the fraction of sequence length consisting
of conserved pairs as a percentage
Returns : scalar float
Args : scalar $type, one of 'hit', 'subject', 'query'
=cut
sub percent_conserved {
my ($self, $type, @args) = @_;
return $self->frac_conserved($type, @args) * 100;
}
=head2 frac_aligned
Title : frac_aligned
Usage : $tiling->frac_aligned($type)
Function: Return the fraction of B<input> sequence length consisting
that was aligned by the algorithm
Returns : scalar float
Args : scalar $type, one of 'hit', 'subject', 'query'
Note : This method must take account of the $type coordinate
system and the length reporting method (see STATISTICS
METHODS above)
=cut
sub frac_aligned{
my ($self, $type, @args) = @_;
$self->throw_not_implemented;
}
# aliases for back compat
sub frac_aligned_query { shift->frac_aligned('query', @_) }
sub frac_aligned_hit { shift->frac_aligned('hit', @_) }
=head2 range
Title : range
Usage : $tiling->range($type)
Function: Returns the extent of the longest tiling
as ($min_coord, $max_coord)
Returns : array of two scalar integers
Args : scalar $type, one of 'hit', 'subject', 'query'
=cut
sub range {
my ($self, $type, @args) = @_;
$self->throw_not_implemented;
}
=head1 TILING ITERATORS
=head2 next_tiling
Title : next_tiling
Usage : @hsps = $self->next_tiling($type);
Function: Obtain a tiling of HSPs over the $type ('hit', 'subject',
'query') sequence
Example :
Returns : an array of HSPI objects
Args : scalar $type: one of 'hit', 'subject', 'query', with
'subject' an alias for 'hit'
=cut
sub next_tiling{
my ($self,$type,@args) = @_;
$self->throw_not_implemented;
}
=head2 rewind_tilings
Title : rewind_tilings
Usage : $self->rewind_tilings($type)
Function: Reset the next_tilings($type) iterator
Example :
Returns : True on success
Args : scalar $type: one of 'hit', 'subject', 'query', with
'subject' an alias for 'hit'
=cut
sub rewind_tilings{
my ($self, $type, @args) = @_;
$self->throw_not_implemented;
}
#alias
sub rewind { shift->rewind_tilings(@_) }
=head1 INFORMATIONAL ACCESSORS
=head2 algorithm
Title : algorithm
Usage : $tiling->algorithm
Function: Retrieve the algorithm name associated with the
invocant's hit object
Returns : scalar string
Args :
=cut
sub algorithm{
my ($self, @args) = @_;
$self->throw_not_implemented;
}
1;