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Bio::Search::HSP::BlastPullHSP.3pm

NAME

Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN hsps

SYNOPSIS

     # 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
                         }
                 }
     }
 
 

DESCRIPTION

This object implements a parser for BlastN hsp 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:

   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::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)
 
 

query

  Title   : query
  Usage   : my $query = $hsp->query
  Function: Returns a SeqFeature representing the query in the HSP
  Returns : L<Bio::SeqFeature::Similarity>
  Args    : none
 
 

hit

  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
 
 

gaps

  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'
 
 

strand

  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 retreive both query and hit together
 
 

start

  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)
 
 

end

  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)
 
 

pvalue

  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