| Bio::Search::HSP::BlastPullHSP(3pm) | User Contributed Perl Documentation | Bio::Search::HSP::BlastPullHSP(3pm) |
Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN hsps
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer_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 hsp 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.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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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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::HSP::BlastNHSP->new();
Function: Builds a new Bio::Search::HSP::BlastNHSP object.
Returns : Bio::Search::HSP::BlastNHSP
Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent)
-parent => Bio::PullParserI object (required if no -chunk)
where the array ref provided to -chunk contains an IO object
for a filehandle to something representing the raw data of the
hsp, and $start and $end define the tell() position within the
filehandle that the hsp data starts and ends (optional; defaults
to start and end of the entire thing described by the filehandle)
Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : L<Bio::SeqFeature::Similarity> Args : none
Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : L<Bio::SeqFeature::Similarity> Args : [optional] new value to set
Title : gaps
Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
Function : Get the number of gap characters in the query, hit, or total alignment.
Returns : Integer, number of gap characters or 0 if none
Args : 'query' = num conserved / length of query seq (without gaps)
'hit' = num conserved / length of hit seq (without gaps)
'total' = num conserved / length of alignment (with gaps)
default = 'total'
Title : strand
Usage : $hsp->strand('query')
Function: Retrieves the strand for the HSP component requested
Returns : +1 or -1 (0 if unknown)
Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject
'query' to retrieve the query strand (default)
'list' or 'array' to retrieve both query and hit together
Title : start
Usage : $hsp->start('query')
Function: Retrieves the start for the HSP component requested
Returns : integer, or list of two integers (query start and subject start) in
list context
Args : 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject
'query' to retrieve the query start (default)
Title : end
Usage : $hsp->end('query')
Function: Retrieves the end for the HSP component requested
Returns : integer, or list of two integers (query end and subject end) in
list context
Args : 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject
'query' to retrieve the query end (default)
Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP Returns : undef (Hmmpfam reports do not have p-values) Args : none
| 2021-08-15 | perl v5.32.1 |