Bio::Search::Tiling::TilingI(3pm) User Contributed Perl Documentation Bio::Search::Tiling::TilingI(3pm)
NAME
Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module
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
",
$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
",
$hit->significance, $tiling->frac_aligned_query, $tiling->num_identical);
}
DESCRIPTION
This module provides strong suggestions for any intended HSP tiling object implementation. An object subclassing TilingI should override
the methods defined here according to their descriptions below.
See the section STATISTICS METHODS for hints on implementing methods that are valid across different algorithms and report types.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Mark A. Jensen
Email maj@fortinbras.us
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
STATISTICS METHODS
The tiling statistics can be thought of as global counterparts to similar statistics defined for the individual HSPs. We therefore
prescribe definitions for many of the synonymous methods defined in Bio::Search::HSP::HSPI.
The tiling statistics must be able to keep track of the coordinate systems in which both the query and subject sequences exist; i.e.,
either nucleotide or amino acid. This information is typically inferred from the name of the algorithm used to perform the original search
(contained in "$hit_object->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.
NCBI BLAST vs WU-BLAST (AB-BLAST) lengths
The total length of the alignment is reported differently between these two flavors. "$hit_object->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").
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, "blastall -m0") or a summary (e.g., "blastall -m8") was parsed. Statistics methods that
depend directly on the sequence data will need to check that that data is present.
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 :
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 :
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'
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)
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'
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)
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'
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)
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'
TILING ITERATORS
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'
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'
INFORMATIONAL ACCESSORS
algorithm
Title : algorithm
Usage : $tiling->algorithm
Function: Retrieve the algorithm name associated with the
invocant's hit object
Returns : scalar string
Args :
perl v5.14.2 2012-03-02 Bio::Search::Tiling::TilingI(3pm)