Bio::Search::Result::HUseraContributed PeBio::Search::Result::HmmpfamResult(3)NAMEBio::Search::Result::HmmpfamResult - A parser and result object for
hmmpfam
results
SYNOPSIS
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
-file => 'result.hmmer');
while (my $result = $in->next_result) {
print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
}
DESCRIPTION
This object implements a parser for hmmpfam result output, a program in
the HMMER package.
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 the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
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 of
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHOR - Sendu Bala
Email bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::SearchIO::Result::hmmpfam->new();
Function: Builds a new Bio::SearchIO::Result::hmmpfam object
Returns : Bio::SearchIO::Result::hmmpfam
Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent)
-parent => Bio::PullParserI object (required if no -chunk)
-parameters => hash ref of search parameters (key => value), optional
-statistics => hash ref of search statistics (key => value), optional
where the array ref provided to -chunk contains an IO object
for a filehandle to something representing the raw data of the
result, and $start and $end define the tell() position within the
filehandle that the result data starts and ends (optional; defaults
to start and end of the entire thing described by the filehandle)
next_hit
Title : next_hit
Usage : while( $hit = $result->next_hit()) { ... }
Function: Returns the next available Hit object, representing potential
matches between the query and various entities from the database.
Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
Args : none
next_model
Title : next_model
Usage : my $domain = $result->next_model
Function: Returns the next domain - this is an alias for next_hit()
Returns : L<Bio::Search::Hit::HitI> object
Args : none
hits
Title : hits
Usage : my @hits = $result->hits
Function: Returns the HitI objects contained within this Result
Returns : Array of Bio::Search::Hit::HitI objects
Args : none
See Also: Bio::Search::Hit::HitI
models
Title : models
Usage : my @domains = $result->models;
Function: Returns the list of HMM models seen - this is an alias for hits()
Returns : Array of L<Bio::Search::Hit::HitI> objects
Args : none
sort_hits
Title : sort_hits
Usage : $result->sort_hits('<score')
Function : Sorts the hits so that they come out in the desired order when
hits() or next_hit() is called.
Returns : n/a
Args : A coderef for the sort function. See the documentation on the Perl
sort() function for guidelines on writing sort functions.
You will be sorting array references, not HitI objects. The
references contain name as element 0, description as element 1,
score as element 2, significance as element 3 and number of hsps
as element 4.
By default the sort order is ascending significance value (ie.
most significant hits first).
Note : To access the special variables $a and $b used by the Perl sort()
function the user function must access
Bio::Search::Result::HmmpfamResult namespace.
For example, use :
$result->sort_hits(
sub{$Bio::Search::Result::HmmpfamResult::a->[2]
<=>
$Bio::Search::Result::HmmpfamResult::b->[2]});
NOT $result->sort_hits($a->[2] <=> $b->[2]);
rewind
Title : rewind
Usage : $result->rewind;
Function: Allow one to reset the Hit iterator to the beginning, so that
next_hit() will subsequently return the first hit and so on.
Returns : n/a
Args : none
perl v5.14.12011-07Bio::Search::Result::HmmpfamResult(3)
