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 temporary solution.