Bio::Search::HSP::FastaHSP(3pm) User Contributed Perl Documentation Bio::Search::HSP::FastaHSP(3pm)NAME
Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data
SYNOPSIS
# get a FastaHSP from a SearchIO stream
my $in = Bio::SearchIO->new(-format => 'fasta', -file => 'filename.fasta');
while( my $r = $in->next_result) {
while( my $hit = $r->next_result ) {
while( my $hsp = $hit->next_hsp ) {
print "smith-waterman score (if available): ",
$hsp->sw_score(),"
";
}
}
}
DESCRIPTION
Describe the object here
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl.org
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::HSP::FastaHSP->new();
Function: Builds a new Bio::Search::HSP::FastaHSP object
Returns : Bio::Search::HSP::FastaHSP
Args : -swscore => smith-waterman score
sw_score
Title : sw_score
Usage : $obj->sw_score($newval)
Function: Get/Set Smith-Waterman score
Returns : value of sw_score
Args : newvalue (optional)
evalue2
Title : evalue2
Usage : $obj->evalue2($newval)
Function: Get/Set E2() expectation value
Returns : value of evalue2
Args : newvalue (optional)
perl v5.14.2 2012-03-02 Bio::Search::HSP::FastaHSP(3pm)
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Bio::Search::Hit::BlastPullHit(3pm) User Contributed Perl Documentation Bio::Search::Hit::BlastPullHit(3pm)NAME
Bio::Search::Hit::BlastPullHit - A parser and hit object for BLASTN hits
SYNOPSIS
# 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, "
";
print $hit->score, "
";
print $hit->significance, "
";
while (my $hsp = $hit->next_hsp) {
# process HSPI objects
}
}
}
DESCRIPTION
This object implements a parser for BLASTN hit output.
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu Bala
Email bix@sendu.me.uk
CONTRIBUTORS
Additional contributors names and emails here
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::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)
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
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
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 HSP iterator to the beginning, so that
next_hsp() will subsequently return the first hsp and so on.
Returns : n/a
Args : none
perl v5.14.2 2012-03-02 Bio::Search::Hit::BlastPullHit(3pm)