Bio::Search::BlastUtils(3pm)				User Contributed Perl Documentation			      Bio::Search::BlastUtils(3pm)

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.

perl v5.14.2							    2012-03-02					      Bio::Search::BlastUtils(3pm)