Bio::Search::Tiling::MapTileUtils - utilities for manipulating closed intervals for an HSP tiling algorithm
Not used directly.
An "interval" in this module is defined as an arrayref [$a0, $a1], where $a0, $a1 are scalar numbers satisfying $a0 <= $a1.
[$a0, $a1]
$a0, $a1
$a0 <= $a1
Mark A. Jensen - maj -at- fortinbras -dot- us
Title : interval_tiling() Usage : @tiling = interval_tiling( \@array_of_intervals ) Function: Find minimal set of intervals covering the input set Returns : array of arrayrefs of the form ( [$interval => [ @indices_of_collapsed_input_intervals ]], ...) Args : arrayref of intervals
Title : decompose_interval Usage : @decomposition = decompose_interval( \@overlappers ) Function: Calculate the disjoint decomposition of a set of overlapping intervals, each annotated with a list of covering intervals Returns : array of arrayrefs of the form ( [[@interval] => [@indices_of_coverers]], ... ) Args : arrayref of intervals (arrayrefs like [$a0, $a1], with Note : Each returned interval is associated with a list of indices of the original intervals that cover that decomposition component (scalar size of this list could be called the 'coverage coefficient') Note : Coverage: each component of the decomp is completely contained in the input intervals that overlap it, by construction. Caveat : This routine expects the members of @overlappers to overlap, but doesn't check this.
Title : are_disjoint Usage : are_disjoint( [$a0, $a1], [$b0, $b1] ) Function: Determine if two intervals are disjoint Returns : True if the intervals are disjoint, false if they overlap Args : array of two intervals
Title : min_covering_interval Usage : $interval = min_covering_interval( [$a0,$a1],[$b0,$b1] ) Function: Determine the minimal covering interval for two intervals Returns : an interval Args : two intervals
Title : get_intervals_from_hsps Usage : @intervals = get_intervals_from_hsps($type, @hsp_objects) Function: Return array of intervals of the form [ $start, $end ], from an array of hsp objects Returns : an array of intervals Args : scalar $type, array of HSPI objects; where $type is one of 'hit', 'subject', 'query'
Title : _allowable_filters Usage : _allowable_filters($Bio_Search_Hit_HitI, $type) Function: Return the HSP filters (strand, frame) allowed, based on the reported algorithm Returns : String encoding allowable filters: s = strand, f = frame Empty string if no filters allowed undef if algorithm unrecognized Args : A Bio::Search::Hit::HitI object, scalar $type, one of 'hit', 'subject', 'query'; default is 'query'
Title : _set_attributes Usage : $tiling->_set_attributes() Function: Sets attributes for invocant that depend on algorithm name Returns : True on success Args : none Note : setting based on the configuration table %alg_lookup
Title : matches_MT Usage : $hsp->matches($type, $action, $start, $end) Purpose : Get the total number of identical or conserved matches in the query or sbjct sequence for the given HSP. Optionally can report data within a defined interval along the seq. Returns : scalar int Args : Comments : Relies on seq_str('match') to get the string of alignment symbols between the query and sbjct lines which are used for determining the number of identical and conservative matches. Note : Modeled on Bio::Search::HSP::HSPI::matches
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.