NAME

Bio::Search::BlastUtils - Utility functions for Bio::Search:: BLAST objects

SYNOPSIS

# This module is just a collection of subroutines, not an object.

See Bio::Search::Hit::BlastHit.

DESCRIPTION

The BlastUtils.pm module is a collection of subroutines used primarily by Bio::Search::Hit::BlastHit objects for some of the additional functionality, such as HSP tiling. Right now, the BlastUtils is just a collection of methods, not an object, and it's tightly coupled to Bio::Search::Hit::BlastHit. A goal for the future is to generalize it to work based on the Bio::Search interfaces, then it can work with any objects that implements them.

AUTHOR

Steve Chervitz <sac@bioperl.org>

tile_hsps

Usage     : tile_hsps( $sbjct );
          : This is called automatically by Bio::Search::Hit::BlastHit 
          : during object construction or
          : as needed by methods that rely on having tiled data.
Purpose   : Collect statistics about the aligned sequences in a set of HSPs.
          : Calculates the following data across all HSPs: 
          :    -- total alignment length 
          :    -- total identical residues 
          :    -- total conserved residues
Returns   : n/a
Argument  : A Bio::Search::Hit::BlastHit object 
Throws    : n/a
Comments  :
	   : This method is *strongly* coupled to Bio::Search::Hit::BlastHit
	   : (it accesses BlastHit data members directly).
	   : TODO: Re-write this to the Bio::Search::Hit::HitI interface.
	   :
          : This method performs more careful summing of data across
          : all HSPs in the Sbjct object. Only HSPs that are in the same strand 
          : and frame are tiled. Simply summing the data from all HSPs
          : in the same strand and frame will overestimate the actual 
          : length of the alignment if there is overlap between different HSPs 
          : (often the case).
          :
          : The strategy is to tile the HSPs and sum over the
          : contigs, collecting data separately from overlapping and
          : non-overlapping regions of each HSP. To facilitate this, the
          : HSP.pm object now permits extraction of data from sub-sections
          : of an HSP.
          : 
          : Additional useful information is collected from the results
          : of the tiling. It is possible that sub-sequences in
          : different HSPs will overlap significantly. In this case, it
          : is impossible to create a single unambiguous alignment by
          : concatenating the HSPs. The ambiguity may indicate the
          : presence of multiple, similar domains in one or both of the
          : aligned sequences. This ambiguity is recorded using the
          : ambiguous_aln() method.
          : 
          : This method does not attempt to discern biologically
          : significant vs. insignificant overlaps. The allowable amount of 
          : overlap can be set with the overlap() method or with the -OVERLAP
          : parameter used when constructing the Blast & Sbjct objects. 
          : 
          : For a given hit, both the query and the sbjct sequences are
          : tiled independently.
          : 
          :    -- If only query sequence HSPs overlap, 
          :          this may suggest multiple domains in the sbjct.
          :    -- If only sbjct sequence HSPs overlap, 
          :          this may suggest multiple domains in the query.
          :    -- If both query & sbjct sequence HSPs overlap, 
          :          this suggests multiple domains in both.
          :    -- If neither query & sbjct sequence HSPs overlap, 
          :          this suggests either no multiple domains in either
          :          sequence OR that both sequences have the same
          :          distribution of multiple similar domains.
          : 
          : This method can deal with the special case of when multiple
          : HSPs exactly overlap.
          : 
          : Efficiency concerns:
          :  Speed will be an issue for sequences with numerous HSPs.
          : 
Bugs      : Currently, tile_hsps() does not properly account for
          : the number of non-tiled but overlapping HSPs, which becomes a problem
          : as overlap() grows. Large values overlap() may thus lead to 
          : incorrect statistics for some hits. For best results, keep overlap()
          : below 5 (DEFAULT IS 2). For more about this, see the "HSP Tiling and
          : Ambiguous Alignments" section in L<Bio::Search::Hit::BlastHit>.

See Also : _adjust_contigs(), Bio::Search::Hit::BlastHit

_adjust_contigs

Usage     : n/a; called automatically during object construction.
Purpose   : Builds HSP contigs for a given BLAST hit.
          : Utility method called by _tile_hsps()
Returns   : 
Argument  : 
Throws    : Exceptions propagated from Bio::Search::Hit::BlastHSP::matches()
          : for invalid sub-sequence ranges.
Status    : Experimental
Comments  : This method does not currently support gapped alignments.
          : Also, it does not keep track of the number of HSPs that
          : overlap within the amount specified by overlap().
          : This will lead to significant tracking errors for large
          : overlap values.

See Also : tile_hsps(), Bio::Search::Hit::BlastHSP::matches

get_exponent

Usage     : &get_exponent( number );
Purpose   : Determines the power of 10 exponent of an integer, float, 
          : or scientific notation number.
Example   : &get_exponent("4.0e-206");
          : &get_exponent("0.00032");
          : &get_exponent("10.");
          : &get_exponent("1000.0");
          : &get_exponent("e+83");
Argument  : Float, Integer, or scientific notation number
Returns   : Integer representing the exponent part of the number (+ or -).
          : If argument == 0 (zero), return value is "-999".
Comments  : Exponents are rounded up (less negative) if the mantissa is >= 5.
          : Exponents are rounded down (more negative) if the mantissa is <= -5.

collapse_nums

Usage     : @cnums = collapse_nums( @numbers );
Purpose   : Collapses a list of numbers into a set of ranges of consecutive terms:
          : Useful for condensing long lists of consecutive numbers.
          :  EXPANDED:
          :     1 2 3 4 5 6 10 12 13 14 15 17 18 20 21 22 24 26 30 31 32
          :  COLLAPSED:
          :     1-6 10 12-15 17 18 20-22 24 26 30-32
Argument  : List of numbers sorted numerically.
Returns   : List of numbers mixed with ranges of numbers (see above).
Throws    : n/a

See Also : Bio::Search::Hit::BlastHit::seq_inds()

strip_blast_html

Usage     : $boolean = &strip_blast_html( string_ref );
          : This method is exported.
Purpose   : Removes HTML formatting from a supplied string.
          : Attempts to restore the Blast report to enable
          : parsing by Bio::SearchIO::blast.pm
Returns   : Boolean: true if string was stripped, false if not.
Argument  : string_ref = reference to a string containing the whole Blast
          :              report containing HTML formatting.
Throws    : Croaks if the argument is not a scalar reference.
Comments  : Based on code originally written by Alex Dong Li
          : (ali@genet.sickkids.on.ca).
          : This method does some Blast-specific stripping 
          : (adds back a '>' character in front of each HSP 
          : alignment listing).
          :   
          : THIS METHOD IS VERY SENSITIVE TO BLAST FORMATTING CHANGES!
          :
          : Removal of the HTML tags and accurate reconstitution of the
          : non-HTML-formatted report is highly dependent on structure of
          : the HTML-formatted version. For example, it assumes that first 
          : line of each alignment section (HSP listing) starts with a
          : <a name=..> anchor tag. This permits the reconstruction of the 
          : original report in which these lines begin with a ">".
          : This is required for parsing.
          :
          : If the structure of the Blast report itself is not intended to
          : be a standard, the structure of the HTML-formatted version
          : is even less so. Therefore, the use of this method to
          : reconstitute parsable Blast reports from HTML-format versions
          : should be considered a temorary solution.