Bio/SearchIO/hmmer.pm

   1 #
   2 # BioPerl module for Bio::SearchIO::hmmer
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Kai Blin <kai.blin@biotech.uni-tuebingen.de>
   7 #
   8 # Copyright Kai Blin
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11 #
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SearchIO::hmmer - A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
  17
  18 =head1 SYNOPSIS
  19
  20     # do not use this class directly it is available through Bio::SearchIO
  21     use Bio::SearchIO;
  22     my $in = Bio::SearchIO->new(-format => 'hmmer',
  23                                -file   => 't/data/L77119.hmmer');
  24     while( my $result = $in->next_result ) {
  25         # this is a Bio::Search::Result::HMMERResult object
  26         print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
  27         while( my $hit = $result->next_hit ) {
  28             print $hit->name(), "\n";
  29             while( my $hsp = $hit->next_hsp ) {
  30                 print "length is ", $hsp->length(), "\n";
  31             }
  32         }
  33     }
  34
  35 =head1 DESCRIPTION
  36
  37 This object implements a parser for HMMER output. It works with both HMMER2 and HMMER3
  38
  39 =head1 FEEDBACK
  40
  41 =head2 Mailing Lists
  42
  43 User feedback is an integral part of the evolution of this and other
  44 Bioperl modules. Send your comments and suggestions preferably to
  45 the Bioperl mailing list.  Your participation is much appreciated.
  46
  47   bioperl-l@bioperl.org                  - General discussion
  48   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  49
  50 =head2 Support
  51
  52 Please direct usage questions or support issues to the mailing list:
  53
  54 I<bioperl-l@bioperl.org>
  55
  56 rather than to the module maintainer directly. Many experienced and
  57 reponsive experts will be able look at the problem and quickly
  58 address it. Please include a thorough description of the problem
  59 with code and data examples if at all possible.
  60
  61 =head2 Reporting Bugs
  62
  63 Report bugs to the Bioperl bug tracking system to help us keep track
  64 of the bugs and their resolution. Bug reports can be submitted via the
  65 web:
  66
  67   https://github.com/bioperl/bioperl-live/issues
  68
  69 =head1 AUTHOR - Kai Blin
  70
  71 Email kai.blin-at-biotech.uni-tuebingen.de
  72
  73 =head1 APPENDIX
  74
  75 The rest of the documentation details each of the object methods.
  76 Internal methods are usually preceded with a _
  77
  78 =cut
  79
  80 # Let the code begin...
  81
  82 package Bio::SearchIO::hmmer;
  83
  84 use strict;
  85
  86 use Bio::Factory::ObjectFactory;
  87
  88 use base qw(Bio::SearchIO);
  89
  90 sub new {
  91   my ( $caller, @args ) = @_;
  92   my $class = ref($caller) || $caller;
  93
  94   my $self = $class->SUPER::new(@args);
  95   $self->_initialize(@args);
  96
  97   # Try to guess the hmmer format version if it's not specified.
  98   my $version;
  99   my %param = @args;
 100
 101   @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
 102
 103   # If the caller specified a version, go for that
 104   if (defined($param{"-version"})) {
 105     $version = $param{"-version"};
 106   } else {
 107
 108     # read second line of the file
 109     my $first_line = $self->_readline;
 110     $_ = $self->_readline;
 111
 112     if ( m/HMMER\s3/ ) {
 113       $version = "3";
 114     } else {
 115       $version = "2";
 116     }
 117
 118     $self->_pushback($_);
 119     $self->_pushback($first_line);
 120   }
 121
 122   my $format = "hmmer$version";
 123   return unless( $class->_load_format_module($format) );
 124
 125   bless($self, "Bio::SearchIO::$format");
 126
 127   return $self;
 128 }
 129
 130 sub _initialize {
 131     my ( $self, @args ) = @_;
 132     $self->SUPER::_initialize(@args);
 133     my $handler = $self->_eventHandler;
 134     $handler->register_factory(
 135         'result',
 136         Bio::Factory::ObjectFactory->new(
 137             -type      => 'Bio::Search::Result::HMMERResult',
 138             -interface => 'Bio::Search::Result::ResultI'
 139         )
 140     );
 141
 142     $handler->register_factory(
 143         'hit',
 144         Bio::Factory::ObjectFactory->new(
 145             -type      => 'Bio::Search::Hit::HMMERHit',
 146             -interface => 'Bio::Search::Hit::HitI'
 147         )
 148     );
 149
 150     $handler->register_factory(
 151         'hsp',
 152         Bio::Factory::ObjectFactory->new(
 153             -type      => 'Bio::Search::HSP::HMMERHSP',
 154             -interface => 'Bio::Search::HSP::HSPI'
 155         )
 156     );
 157 }
 158
 159 1;