---
name: "Bio::Search::HSP::HmmpfamHSP"
section: "3pm"
platform: "linux"
package: "libbio-searchio-hmmer-perl"
version: "1.7.3-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Search::HSP::HmmpfamHSP"
---

# Bio::Search::HSP::HmmpfamHSP(3pm)

A parser and HSP object for hmmpfam hsps

## NAME

Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps

## SYNOPSIS

```
    # 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
                        }
                }
    }
```

## DESCRIPTION

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

## 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://github.com/bioperl/bioperl-live/issues
```

## 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::HmmpfamHSP->new();
 Function: Builds a new Bio::Search::HSP::HmmpfamHSP object.
 Returns : Bio::Search::HSP::HmmpfamHSP
 Args    : -chunk  => [Bio::Root::IO, $start, $end] (required if no -parent)
           -parent => Bio::PullParserI object (required if no -chunk)
           -hsp_data => array ref with [rank query_start query_end hit_start
                                                                                hit_end score evalue]
           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 gaps in the query, hit, or total alignment.
 Returns  : Integer, number of gaps 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'
```

### 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
```