NAME¶
Bio::Search::Hit::HmmpfamHit - A parser and hit object for hmmpfam hits
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) {
while (my $hit = $result->next_hit) {
print $hit->name, "\n";
print $hit->score, "\n";
print $hit->significance, "\n";
while (my $hsp = $hit->next_hsp) {
# process HSPI objects
}
}
}
DESCRIPTION¶
This object implements a parser for hmmpfam hit 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:
https://github.com/bioperl/bioperl-live/issues
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::Search::Hit::HmmpfamHit->new();
Function: Builds a new Bio::Search::Hit::HmmpfamHit object.
Returns : Bio::Search::Hit::HmmpfamHit
Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent)
-parent => Bio::PullParserI object (required if no -chunk)
-hit_data => array ref with [name description score significance
num_hsps rank]
where the array ref provided to -chunk contains an IO object
for a filehandle to something representing the raw data of the
hit, and $start and $end define the tell() position within the
filehandle that the hit data starts and ends (optional; defaults
to start and end of the entire thing described by the filehandle)
next_hsp¶
Title : next_hsp
Usage : while( $hsp = $obj->next_hsp()) { ... }
Function : Returns the next available High Scoring Pair
Example :
Returns : L<Bio::Search::HSP::HSPI> object or null if finished
Args : none
next_domain¶
Title : next_domain
Usage : my $domain = $hit->next_domain();
Function: An alias for L<next_hsp()>, this will return the next HSP
Returns : L<Bio::Search::HSP::HSPI> object
Args : none
hsps¶
Usage : $hit_object->hsps();
Purpose : Get a list containing all HSP objects.
Example : @hsps = $hit_object->hsps();
Returns : list of L<Bio::Search::HSP::BlastHSP> objects.
Argument : none
domains¶
Title : domains
Usage : my @domains = $hit->domains();
Function: An alias for L<hsps()>, this will return the full list of hsps
Returns : array of L<Bio::Search::HSP::HSPI> objects
Args : none
hsp¶
Usage : $hit_object->hsp( [string] );
Purpose : Get a single HSPI object for the present HitI object.
Example : $hspObj = $hit_object->hsp; # same as 'best'
: $hspObj = $hit_object->hsp('best');
: $hspObj = $hit_object->hsp('worst');
Returns : Object reference for a L<Bio::Search::HSP::HSPI> object.
Argument : String (or no argument).
: No argument (default) = highest scoring HSP (same as 'best').
: 'best' = highest scoring HSP.
: 'worst' = lowest scoring HSP.
Throws : Exception if an unrecognized argument is used.
See Also :
hsps(), num_hsps()
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
strand¶
Usage : $sbjct->strand( [seq_type] );
Purpose : Gets the strand(s) for the query, sbjct, or both sequences.
: For hmmpfam, the answers are always 1 (forward strand).
Example : $qstrand = $sbjct->strand('query');
: $sstrand = $sbjct->strand('hit');
: ($qstrand, $sstrand) = $sbjct->strand();
Returns : scalar context: integer '1'
: array context without args: list of two strings (1, 1)
: Array context can be "induced" by providing an argument of 'list'
: or 'array'.
Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default
: = 'query') ('sbjct' is synonymous with 'hit')
frac_aligned_query¶
Usage : $hit_object->frac_aligned_query();
Purpose : Get the fraction of the query sequence which has been aligned
: across all HSPs (not including intervals between non-overlapping
: HSPs).
Example : $frac_alnq = $hit_object->frac_aligned_query();
Returns : undef (the length of query sequences is unknown in Hmmpfam reports)
Argument : none