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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.