| Bio::Search::Hit::BlastPullHit(3pm) | User Contributed Perl Documentation | Bio::Search::Hit::BlastPullHit(3pm) |
Bio::Search::Hit::BlastPullHit - A parser and hit object for BLASTN hits
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'blast_pull',
-file => 'result.blast');
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
}
}
}
This object implements a parser for BLASTN hit output.
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.
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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.
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:
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Additional contributors names and emails here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : my $obj = Bio::Search::Hit::BlastNHit->new();
Function: Builds a new Bio::Search::Hit::BlastNHit object.
Returns : Bio::Search::Hit::BlastNHit
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]
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)
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
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
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()
Title : rewind
Usage : $result->rewind;
Function: Allow one to reset the HSP iterator to the beginning, so that
next_hsp() will subsequently return the first hsp and so on.
Returns : n/a
Args : none
| 2018-10-27 | perl v5.26.2 |