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Bio::Search::Hit::HmmpfamHit(3pm) User Contributed Perl Documentation Bio::Search::Hit::HmmpfamHit(3pm)


Bio::Search::Hit::HmmpfamHit - A parser and hit object for hmmpfam hits


    # 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


This object implements a parser for hmmpfam hit output, a program in the HMMER package.


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Please direct usage questions or support issues to the mailing list:

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.

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AUTHOR - Sendu Bala



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::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)


 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


 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


 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


 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


 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 Hit iterator to the beginning, so that
           next_hit() will subsequently return the first hit and so on.
 Returns : n/a
 Args    : none


 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')


 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
2018-10-27 perl v5.26.2