lib/Bio/DB/EMBL.pm

   1 #
   2 #
   3 # BioPerl module for Bio::DB::EMBL
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
   8 #
   9 # Copyright Jason Stajich
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::DB::EMBL - Database object interface for EMBL entry retrieval
  18
  19 =head1 SYNOPSIS
  20
  21   use Bio::DB::EMBL;
  22
  23   $embl = Bio::DB::EMBL->new();
  24
  25   # remember that EMBL_ID does not equal GenBank_ID!
  26   $seq = $embl->get_Seq_by_id('HSFOS'); # EMBL ID
  27   print "cloneid is ", $seq->id, "\n";
  28
  29   # or changeing to accession number and Fasta format ...
  30   $embl->request_format('fasta');
  31   $seq = $embl->get_Seq_by_acc('J02231'); # EMBL ACC
  32   print "cloneid is ", $seq->id, "\n";
  33
  34   # especially when using versions, you better be prepared
  35   # in not getting what what want
  36   eval {
  37       $seq = $embl->get_Seq_by_version('J02231.1'); # EMBL VERSION
  38   };
  39   print "cloneid is ", $seq->id, "\n" unless $@;
  40
  41   # or ... best when downloading very large files, prevents
  42   # keeping all of the file in memory
  43
  44   # also don't want features, just sequence so let's save bandwidth
  45   # and request Fasta sequence
  46   $embl = Bio::DB::EMBL->new(-retrievaltype => 'tempfile' ,
  47                             -format => 'fasta');
  48   my $seqio = $embl->get_Stream_by_id(['AC013798', 'AC021953'] );
  49   while( my $clone =  $seqio->next_seq ) {
  50         print "cloneid is ", $clone->id, "\n";
  51   }
  52
  53 =head1 DESCRIPTION
  54
  55 Allows the dynamic retrieval of sequence objects L<Bio::Seq> from the
  56 EMBL database using the dbfetch script at EBI:
  57 L<http://www.ebi.ac.uk/Tools/dbfetch/dbfetch>.
  58
  59 In order to make changes transparent we have host type (currently only
  60 ebi) and location (defaults to ebi) separated out.  This allows later
  61 additions of more servers in different geographical locations.
  62
  63 The functionality of this module is inherited from L<Bio::DB::DBFetch>
  64 which implements L<Bio::DB::WebDBSeqI>.
  65
  66 =head1 FEEDBACK
  67
  68 =head2 Mailing Lists
  69
  70 User feedback is an integral part of the evolution of this and other
  71 Bioperl modules. Send your comments and suggestions preferably to one
  72 of the Bioperl mailing lists.  Your participation is much appreciated.
  73
  74   bioperl-l@bioperl.org                  - General discussion
  75   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  76
  77 =head2 Support
  78
  79 Please direct usage questions or support issues to the mailing list:
  80
  81 I<bioperl-l@bioperl.org>
  82
  83 rather than to the module maintainer directly. Many experienced and
  84 reponsive experts will be able look at the problem and quickly
  85 address it. Please include a thorough description of the problem
  86 with code and data examples if at all possible.
  87
  88 =head2 Reporting Bugs
  89
  90 Report bugs to the Bioperl bug tracking system to help us keep track
  91 the bugs and their resolution.  Bug reports can be submitted via the
  92 web:
  93
  94   https://github.com/bioperl/bioperl-live/issues
  95
  96 =head1 AUTHOR - Heikki Lehvaslaiho
  97
  98 Email Heikki Lehvaslaiho E<lt>heikki-at-bioperl-dot-orgE<gt>
  99
 100 =head1 APPENDIX
 101
 102 The rest of the documentation details each of the object
 103 methods. Internal methods are usually preceded with a _
 104
 105 =cut
 106
 107 # Let the code begin...
 108
 109 package Bio::DB::EMBL;
 110 use strict;
 111 use vars qw($MODVERSION %HOSTS %FORMATMAP  $DEFAULTFORMAT);
 112
 113 $MODVERSION = '0.2';
 114 use Bio::DB::RefSeq;
 115
 116 use base qw(Bio::DB::DBFetch);
 117
 118 BEGIN {
 119     # you can add your own here theoretically.
 120     %HOSTS = (
 121                'dbfetch' => {
 122                    baseurl => 'http://%s/Tools/dbfetch/dbfetch?db=embl&style=raw',
 123                    hosts   => {
 124                        'ebi'  => 'www.ebi.ac.uk'
 125                        }
 126                }
 127               );
 128     %FORMATMAP = ( 'embl' => 'embl',
 129                    'fasta' => 'fasta'
 130                    );
 131     $DEFAULTFORMAT = 'embl';
 132 }
 133
 134 =head2 new
 135
 136  Title   : new
 137  Usage   : $gb = Bio::DB::GenBank->new(@options)
 138  Function: Creates a new genbank handle
 139  Returns : New genbank handle
 140  Args    : -delay   number of seconds to delay between fetches (3s)
 141
 142 NOTE:  There are other options that are used internally.
 143
 144 =cut
 145
 146 sub new {
 147     my ($class, @args ) = @_;
 148     my $self = $class->SUPER::new(@args);
 149
 150     $self->{ '_hosts' } = {};
 151     $self->{ '_formatmap' } = {};
 152
 153     $self->hosts(\%HOSTS);
 154     $self->formatmap(\%FORMATMAP);
 155     $self->{'_default_format'} = $DEFAULTFORMAT;
 156
 157     return $self;
 158 }
 159
 160
 161 =head2 Bio::DB::WebDBSeqI methods
 162
 163 Overriding WebDBSeqI method to help newbies to retrieve sequences.
 164 EMBL database is all too often passed RefSeq accessions. This
 165 redirects those calls. See L<Bio::DB::RefSeq>.
 166
 167
 168 =head2 get_Stream_by_acc
 169
 170   Title   : get_Stream_by_acc
 171   Usage   : $seq = $db->get_Seq_by_acc([$acc1, $acc2]);
 172   Function: Gets a series of Seq objects by accession numbers
 173   Returns : a Bio::SeqIO stream object
 174   Args    : $ref : a reference to an array of accession numbers for
 175                    the desired sequence entries
 176   Note    : For GenBank, this just calls the same code for get_Stream_by_id()
 177
 178 =cut
 179
 180 sub get_Stream_by_acc {
 181     my ($self, $ids ) = @_;
 182     my $newdb = $self->_check_id($ids);
 183     if ($newdb && $newdb->isa('Bio::DB::RefSeq')) {
 184         return $newdb->get_seq_stream('-uids' => $ids, '-mode' => 'single');
 185     } else {
 186         return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single');
 187     }
 188 }
 189
 190
 191 =head2 _check_id
 192
 193   Title   : _check_id
 194   Usage   :
 195   Function:
 196   Returns : A Bio::DB::RefSeq reference or throws
 197   Args    : $id(s), $string
 198
 199 =cut
 200
 201 sub _check_id {
 202     my ($self, $ids) = @_;
 203
 204     # NT contigs can not be retrieved
 205     $self->throw("NT_ contigs are whole chromosome files which are not part of regular".
 206                  "database distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.")
 207         if $ids =~ /NT_/;
 208
 209     # Asking for a RefSeq from EMBL/GenBank
 210
 211     if ($ids =~ /N._/) {
 212         $self->warn("[$ids] is not a normal sequence entry but a RefSeq entry.".
 213                    " Redirecting the request.\n")
 214             if $self->verbose >= 0;
 215         return  Bio::DB::RefSeq->new(-verbose => $self->verbose);
 216     }
 217 }
 218
 219
 220 1;