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.\" ========================================================================
.\"
.IX Title "Bio::SearchIO::hmmer 3pm"
.TH Bio::SearchIO::hmmer 3pm "2019-10-29" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::SearchIO::hmmer \- A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 10
\&    # do not use this class directly it is available through Bio::SearchIO
\&    use Bio::SearchIO;
\&    my $in = Bio::SearchIO\->new(\-format => \*(Aqhmmer\*(Aq,
\&                               \-file   => \*(Aqt/data/L77119.hmmer\*(Aq);
\&    while( my $result = $in\->next_result ) {
\&        # this is a Bio::Search::Result::HMMERResult object
\&        print $result\->query_name(), " for HMM ", $result\->hmm_name(), "\en";
\&        while( my $hit = $result\->next_hit ) {
\&            print $hit\->name(), "\en";
\&            while( my $hsp = $hit\->next_hsp ) {
\&                print "length is ", $hsp\->length(), "\en";
\&            }
\&        }
\&    }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object implements a parser for \s-1HMMER\s0 output. It works with both \s-1HMMER2\s0 and \s-1HMMER3\s0
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Kai Blin"
.IX Header "AUTHOR - Kai Blin"
Email kai.blin\-at\-biotech.uni\-tuebingen.de
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _