NAME
Bio::Search::Iteration::IterationI - Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.
SYNOPSIS
# Bio::Search::Iteration::IterationI objects cannot be
# instantiated since this module defines a pure interface.
# Given an object that implements the
# Bio::Search::Iteration::IterationI interface,
# you can do the following things with it:
# First, open up a SearchIO stream
use Bio::SearchIO;
my $file = shift or die "Usage: $0 <BLAST-report-file>\n";
my $in = Bio::SearchIO->new(-format => 'blast',
-file => $file # comment out this line to read STDIN
);
# Iterate over all results in the input stream
while (my $result = $in->next_result) {
printf "Result #%d: %s\n", $in->result_count, $result->to_string;
printf "Total Iterations: %d\n", $result->num_iterations();
# Iterate over all iterations and process old and new hits
# separately.
while( my $it = $result->next_iteration) {
printf "\nIteration %d\n", $it->number;
printf "Converged: %d\n", $it->converged;
# Print out the hits not found in previous iteration
printf "New hits: %d\n", $it->num_hits_new;
while( my $hit = $it->next_hit_new ) {
printf " %s, Expect=%g\n", $hit->name, $hit->expect;
}
# Print out the hits found in previous iteration
printf "Old hits: %d\n", $it->num_hits_old;
while( my $hit = $it->next_hit_old ) {
printf " %s, Expect=%g\n", $hit->name, $hit->expect;
}
}
printf "%s\n\n", '-' x 50;
}
printf "Total Reports processed: %d: %s\n", $in->result_count;
__END__
# NOTE: The following functionality is just proposed
# (does not yet exist but might, given sufficient hew and cry):
# Zero-in on the new hits found in last iteration.
# By default, iteration() returns the last one.
my $last_iteration = $result->iteration();
while( my $hit = $last_iteration->next_hit) {
# Do something with new hit...
}
# Get the first iteration
my $first_iteration = $result->iteration(1);DESCRIPTION
Bio::Search::Result::ResultI objects are data structures containing the results from the execution of a search algorithm. As such, it may contain various algorithm specific information as well as details of the execution, but will contain a few fundamental elements, including the ability to return Bio::Search::Hit::HitI objects.
Classification of Hits
Within a given iteration, the hits can be classified into a number of useful subsets based on whether or not the hit appeard in a previous iteration and whether or not the hit is below the threshold E-value for inclusion in the score matrix model.
All hits
(A)
_______________|_________________
| |
New hits Old hits
(B) (C)
_________|________ _______|_________
| | | |
Below Above Below Above
threshold threshold threshold threshold
(D) (E) (F) (G)
_________|___________
| |
Occurred in a Occurred in a
previous iteration previous iteration
below threshold above threshold
(H) (I)Notes: The term threshold in the diagram and descriptions below refer to this inclusion threshold. Below threshold actually means at or below threshold.
The IterationI interface defines a number of methods for extracting these subsets of hits.
newhits_below_threshold() [subset D]
Hits that did not appear in a previous iteration and are below threshold in the current iteration.
newhits_not_below_threshold() [subset E]
Hits that did not appear in a previous iteration and are not below threshold in the current iteration.
newhits() [subset B]
All newly found hits, below and above the inclusion threshold. This is the union of newhits_below_threshold() + newhits_not_below_threshold() [subset D + subset E].
oldhits_below_threshold() [subset H]
Hits that appeared in a previous iteration below threshold and are still below threshold in the current iteration.
oldhits_newly_below_threshold() [subset I]
Hits that appeared in a previous iteration above threshold but are below threshold in the current iteration. (Not applicable to the first iteration.)
oldhits_not_below_threshold() [subset G]
Hits that appeared in a previous iteration not below threshold and are still not below threshold in the current iteration.
oldhits() [subset C]
All hits that occured in a previous iteration, whether below or above threshold in the current iteration. Union of oldhits_below_threshold() + oldhits_newly_below_threshold() + oldhits_not_below_threshold() [subset H + subset I + subset G]. (Not applicable to the first iteration.)
hits_below_threshold() [subset D + subset F]
All hits, old and new, that are below the inclusion threshold in this iteration. This is the union of newhits_below_threshold() + oldhits_below_threshold() + oldhits_newly_below_threshold() [subset D + subset H + subset I].
hits() [subset A]
The union of newhits() and oldhits() [subset B + subset C].
For the first iteration, the methods oldhits, oldhits_below_threshold, oldhits_newly_below_threshold, and oldhits_not_below_threshold() will return empty lists.
Iterator and numbers-of-hit methods are provided for subsets A, B, and C:
next_hit_new(), num_hits_new() [subset B]
next_hit_old(), num_hits_old() [subset C]
next_hit(), num_hits() [subset A]
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing listsSupport
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issuesAUTHOR
Steve Chervitz <sac@bioperl.org>
See the FEEDBACK section for where to send bug reports and comments.
COPYRIGHT
Copyright (c) 2003 Steve Chervitz. All Rights Reserved.
DISCLAIMER
This software is provided "as is" without warranty of any kind.
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
number
Title : number
Usage : $it_number = $iteration->number();
Purpose : returns the number of the iteration (a.k.a "round")
within the Result.
Returns : integer
Args : [optional] integer to set the number of the iterationconverged
Title : converged
Usage : $it_converged = $iteration->converged();
Purpose : Indicates whether or not the iteration has converged
Returns : boolean
Args : [optional] boolean value to set the converged of the iterationnext_hit
Title : next_hit
Usage : while( $hit = $iteration->next_hit( [$found_again]) ) { ... }
Purpose : Iterates through all of the HitI objects
including new hits and old hits found in a previous iteration
and both below and above the inclusion threshold.
Corresponds to subset A in the "Classification of Hits"
documentation section of this module.
Returns : A Bio::Search::Hit::HitI object or undef if there are no more.
Hits will be returned in the order in which they occur in the report
unless otherwise specified.
Args : noneSee Also: hits, "Classification of Hits"
next_hit() iterates through all hits, including the new ones for this iteration and those found in previous iterations. You can interrogate each hit using Bio::Search::Hit::HitI::found_again to determine whether it is new or old.
To get just the new hits, use next_hit_new. To get just the old hits, use next_hit_old.
next_hit_new
Title : next_hit_new
Usage : while( $hit = $iteration->next_hit_new() ) { ... }
Purpose : Iterates through all newly found hits (did not occur in a
previous iteration) and are either below or above the inclusion threshold.
Corresponds to subset B in the "Classification of Hits"
documentation section of this module.
Returns : A Bio::Search::Hit::HitI object or undef if there are no more.
Hits will be returned in the order in which they occur in the report
unless otherwise specified.
Args : noneSee Also: next_hit, next_hit_old, newhits, "Classification of Hits"
next_hit_old
Title : next_hit_old
Usage : while( $hit = $iteration->next_hit_old() ) { ... }
Purpose : Iterates through the Hit objects representing just the
hits that have been found in a previous iteration, whether
below or above the inclusion threshold.
Corresponds to subset C in the "Classification of Hits"
documentation section of this module.
Returns : A Bio::Search::Hit::HitI object or undef if there are no more.
Hits will be returned in the order in which they occur in the report
unless otherwise specified.
Args : noneSee Also: next_hit, next_hit_old, oldhits, "Classification of Hits"
num_hits
Title : num_hits
Usage : my $hitcount_total = $iteration->num_hits
Purpose : Returns the total number of hits for this query result, including new and old
below and above inclusion threshold.
Returns : integer
Args : noneSee Also: num_hits_new, num_hits_old, "Classification of Hits"
num_hits_new
Title : num_hits_new
Usage : my $hitcount_new = $result->num_hits_new;
: my $hitcount_new_below_thresh = $result->num_hits_new( 1 );
Purpose : Returns the number of new hits in this iteration that were not
found in a previous iteration and are either below or above the
the inclusion threshold.
Corresponds to subset B in the "Classification of Hits"
documentation section of this module.
Returns : integer
Args : (optional) boolean, true if you want to get a count of just the new hits
that are below the inclusion threshold.See Also: num_hits, num_hits_old, "Classification of Hits"
num_hits_old
Title : num_hits_old
Usage : my $hitcount_old = $result->num_hits_old;
: my $hitcount_old_below_thresh = $result->num_hits_old( 1 );
Purpose : Returns the number of new hits in this iteration that were
found in a previous iteration and are either below or above the
the inclusion threshold.
Corresponds to subset C in the "Classification of Hits"
documentation section of this module.
Returns : integer
Args : (optional) boolean, true if you want to get a count of just the old hits
that are below the inclusion threshold.See Also: num_hits, num_hits_new, "Classification of Hits"
hits
Title : hits
Usage : foreach( $obj->hits() ) { ... };
Purpose : Provides access to all hits, both new and old, and either
below or above the inclusion threshold.
Corresponds to subset A in the "Classification of Hits"
documentation section of this module.
Returns : An array containing all HitI objects.
Hits will be ordered according to their occurrence in the report
unless otherwise specified.
Args : noneSee Also: newhits, oldhits, "Classification of Hits"
newhits
Title : newhits
Usage : foreach( $obj->newhits() ) { ... };
Purpose : Provides access to hits that were not found in a previous iteration
and may be either below or above the inclusion threshold.
Corresponds to subset B in the "Classification of Hits"
documentation section of this module.
Returns : An array containing Bio::Search::Hit::HitI objects.
Hits will be ordered according to their occurrence in the report
unless otherwise specified.
Args : noneSee Also: hits, oldhits, newhits_below_threshold + newhits_not_below_threshold, "Classification of Hits"
oldhits
Title : oldhits
Usage : foreach( $obj->oldhits() ) { ... };
Purpose : Provides access to hits that were found in a previous iteration
and are either below or above the inclusion threshold in the current iteration.
Corresponds to subset C in the "Classification of Hits"
documentation section of this module.
Returns : An array containing Bio::Search::Hit::HitI objects.
Hits will be ordered according to their occurrence in the report
unless otherwise specified.
Args : noneSee Also: hits, newhits, oldhits_below_threshold, oldhits_newly_below_threshold, oldhits_not_below_threshold, "Classification of Hits"
newhits_below_threshold
Title : newhits_below_threshold
Usage : foreach( $obj->newhits_below_threshold() ) { ... };
Purpose : Provides access to hits that did not appear in a
previous iteration and are below threshold.
Corresponds to subset D in the "Classification of Hits"
documentation section of this module.
Returns : An array containing Bio::Search::Hit::HitI objects.
Hits will be returned in the order in which they occur in the report
unless otherwise specified.
Args : noneSee Also: newhits_not_below_threshold, oldhits_newly_below_threshold, newhits, "Classification of Hits"
oldhits_below_threshold
Title : oldhits_below_threshold
Usage : foreach( $obj->oldhits_below_threshold() ) { ... };
Purpose : Provides access to hits that appeared in a
previous iteration below inclusion threshold and are still below threshold.
Corresponds to subset H in the "Classification of Hits"
documentation section of this module.
Returns : An array containing Bio::Search::Hit::HitI objects.
Hits will be returned in the order in which they occur in the report
unless otherwise specified.
Args : noneSee Also: oldhits_not_below_threshold, oldhits_newly_below_threshold, oldhits, "Classification of Hits"
oldhits_newly_below_threshold
Title : oldhits_newly_below_threshold
Usage : foreach( $obj->oldhits_newly_below_threshold() ) { ... };
Purpose : Provides access to hits that appeared in a previous
iteration above threshold but are below threshold in the
current iteration. Not applicable to the first iteration.
Corresponds to subset I in the "Classification of Hits"
documentation section of this module.
Returns : An array containing Bio::Search::Hit::HitI objects.
Hits will be returned in the order in which they occur in the report
unless otherwise specified.
Args : noneSee Also: newhits_below_threshold, oldhits, "Classification of Hits"
oldhits_not_below_threshold
Title : oldhits_not_below_threshold
Usage : foreach( $obj->oldhits_not_below_threshold() ) { ... };
Purpose : Provides access to hits that appeared in a previous iteration
not below threshold and are still not below threshold.
Corresponds to subset G in the "Classification of Hits"
documentation section of this module.
Returns : An array containing Bio::Search::Hit::HitI objects.
Hits will be returned in the order in which they occur in the report
unless otherwise specified.
Args : noneSee Also: oldhits_below_threshold, oldhits, "Classification of Hits"
newhits_not_below_threshold
Title : newhits_not_below_threshold
Usage : foreach( $obj->newhits_not_below_threshold() ) { ... };
Purpose : Provides access to hits that did not appear in a
previous iteration and are not below threshold
in the current iteration.
Corresponds to subset E in the "Classification of Hits"
documentation section of this module.
Returns : An array containing Bio::Search::Hit::HitI objects.
Hits will be returned in the order in which they occur in the report
unless otherwise specified.
Args : noneSee Also: newhits_below_threshold, newhits, "Classification of Hits"
hits_below_threshold
Title : hits_below_threshold
Usage : foreach( $obj->hits_below_threshold() ) { ... };
Purpose : Provides access to all hits, old and new, that are below the inclusion threshold.
Corresponds to the union of subset D and subset F in the
"Classification of Hits" documentation section of this module.
Returns : An array containing Bio::Search::Hit::HitI objects.
Hits will be returned in the order in which they occur in the report
unless otherwise specified.
Args : noneSee Also: newhits_below_threshold, oldhits_newly_below_threshold, oldhits_below_threshold, "Classification of Hits"
add_hit
Title : add_hit
Usage : $report->add_hit(-hit =>$hit_obj,
-old =>$boolean,
-below_threshold =>$boolean,
-newly_below =>$boolean )
Purpose : Adds a HitI to the stored list of hits
Returns : Number of HitI currently stored for the class of the added hit.
Args : Tagged values, the only required one is -hit. All others are used
only for PSI-BLAST reports.
-hit => Bio::Search::Hit::HitI object
-old => boolean, true indicates that the hit was found
in a previous iteration. Default=false.
-below_threshold => boolean, true indicates that the hit is below
the inclusion threshold.
-newly_below => boolean, true indicates that the hit is below
the inclusion threshold in this iteration but was above
the inclusion threshold in a previous iteration.
Only appropriate for old hits. Default=false.
Throws : Bio::Root::BadParameter if the hit is not a
Bio::Search::Hit::HitI.
Bio::Root::BadParameter if -old=>false and -newly_below=>true.get_hit
Title : get_hit
Usage : $hit = $report->get_hit( $hit_name )
Purpose : Gets a HitI object given its name
if a hit with this name exists within this Iteration.
Returns : Bio::Search::Hit::HitI object or undef if there is no such hit.
Args : $hit_name = string containing name of the hit
Throws : n/aThe name string must be the same as that returned by Bio::Search::Hit::HitI::name().
The lookup should be case-insensitive.