Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module
Not used directly. Useful POD here for developers, however.
The interface is designed 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); }
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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.
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 :
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 :
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'
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)
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'
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)
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'
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)
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'
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'
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'
Title : algorithm Usage : $tiling->algorithm Function: Retrieve the algorithm name associated with the invocant's hit object Returns : scalar string Args :