Mercurial > repos > mahtabm > ensembl
comparison variant_effect_predictor/Bio/DB/XEMBL.pm @ 0:1f6dce3d34e0
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author | mahtabm |
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date | Thu, 11 Apr 2013 02:01:53 -0400 |
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-1:000000000000 | 0:1f6dce3d34e0 |
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1 # | |
2 # $Id: XEMBL.pm,v 1.3 2002/10/22 07:38:29 lapp Exp $ | |
3 # | |
4 # BioPerl module for Bio::DB::XEMBL | |
5 # | |
6 # Cared for by Lincoln Stein | |
7 # | |
8 # Copyright Lincoln Stein | |
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::DB::XEMBL - Database object interface for XEMBL entry retrieval | |
17 | |
18 =head1 SYNOPSIS | |
19 | |
20 use Bio::DB::XEMBL; | |
21 | |
22 $embl = new Bio::DB::XEMBL; | |
23 | |
24 # remember that XEMBL_ID does not equal GenBank_ID! | |
25 $seq = $embl->get_Seq_by_id('BUM'); # EMBL ID | |
26 print "cloneid is ", $seq->id, "\n"; | |
27 | |
28 # or changeing to accession number and Fasta format ... | |
29 $seq = $embl->get_Seq_by_acc('J02231'); # XEMBL ACC | |
30 print "cloneid is ", $seq->id, "\n"; | |
31 | |
32 # especially when using versions, you better be prepared | |
33 # in not getting what what want | |
34 eval { | |
35 $seq = $embl->get_Seq_by_version('J02231.1'); # XEMBL VERSION | |
36 } | |
37 print "cloneid is ", $seq->id, "\n" unless $@; | |
38 | |
39 my $seqio = $embl->get_Stream_by_batch(['U83300','U83301','U83302']); | |
40 while( my $clone = $seqio->next_seq ) { | |
41 print "cloneid is ", $clone->id, "\n"; | |
42 } | |
43 | |
44 =head1 DESCRIPTION | |
45 | |
46 Allows the dynamic retrieval of Bio::Seq objects from the XEMBL | |
47 database. See L<Bio::Seq> for details. | |
48 | |
49 =head1 FEEDBACK | |
50 | |
51 =head2 Mailing Lists | |
52 | |
53 User feedback is an integral part of the evolution of this and other | |
54 Bioperl modules. Send your comments and suggestions preferably to one | |
55 of the Bioperl mailing lists. Your participation is much appreciated. | |
56 | |
57 bioperl-l@bioperl.org - General discussion | |
58 http://bio.perl.org/MailList.html - About the mailing lists | |
59 | |
60 =head2 Reporting Bugs | |
61 | |
62 Report bugs to the Bioperl bug tracking system to help us keep track | |
63 the bugs and their resolution. | |
64 Bug reports can be submitted via email or the web: | |
65 | |
66 bioperl-bugs@bio.perl.org | |
67 http://bugzilla.bioperl.org/ | |
68 | |
69 =head1 AUTHOR - Lincoln Stein | |
70 | |
71 Email Lincoln Stein E<lt>lstein@cshl.orgE<gt> | |
72 | |
73 =head1 APPENDIX | |
74 | |
75 The rest of the documentation details each of the object | |
76 methods. Internal methods are usually preceded with a _ | |
77 | |
78 =cut | |
79 | |
80 # Let the code begin... | |
81 | |
82 package Bio::DB::XEMBL; | |
83 use strict; | |
84 use Bio::DB::RandomAccessI; | |
85 use Bio::DB::XEMBLService 'getNucSeq'; | |
86 # bsml parser appears broken... | |
87 use Bio::SeqIO::bsml; | |
88 use File::Temp 'tempfile'; | |
89 use vars qw(@ISA $MODVERSION); | |
90 | |
91 @ISA = qw(Bio::DB::RandomAccessI); | |
92 $MODVERSION = '0.1'; | |
93 | |
94 sub new { | |
95 my ($class, @args ) = @_; | |
96 my $self = $class->SUPER::new(@args); | |
97 return $self; | |
98 } | |
99 | |
100 =head2 get_Seq_by_id | |
101 | |
102 Title : get_Seq_by_id | |
103 Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') | |
104 Function: Gets a Bio::Seq object by its name | |
105 Returns : a Bio::Seq object | |
106 Args : the id (as a string) of a sequence | |
107 Throws : "id does not exist" exception | |
108 | |
109 | |
110 =cut | |
111 | |
112 sub get_Seq_by_id { | |
113 my ($self,@args) = @_; | |
114 my $seqio = $self->get_Stream_by_batch([@args]); | |
115 return $seqio->next_seq; | |
116 } | |
117 | |
118 =head2 get_Stream_by_batch | |
119 | |
120 Title : get_Stream_by_batch | |
121 Usage : $seq = $db->get_Stream_by_batch($ref); | |
122 Function: Retrieves Seq objects from XEMBL 'en masse', rather than one | |
123 at a time. Currently this is not particularly efficient, as | |
124 it loads the entire result into memory and parses it. | |
125 Example : | |
126 Returns : a Bio::SeqIO stream object | |
127 Args : $ref : an array reference containing a list of unique | |
128 ids/accession numbers. | |
129 | |
130 =cut | |
131 | |
132 sub get_Stream_by_batch { | |
133 my ($self, $ids) = @_; | |
134 $self->throw("expected an array ref, but got $ids") | |
135 unless ref($ids) eq 'ARRAY'; | |
136 my @args = @$ids; | |
137 my $result = getNucSeq(SOAP::Data->name(format=>'bsml'), | |
138 SOAP::Data->name(ids=>"@args")) | |
139 or $self->throw('id does not exist'); | |
140 my($fh,$filename) = tempfile(File::Spec->tmpdir . '/bsmlXXXXXX',SUFFIX=>'.bsml'); | |
141 print $fh $result; | |
142 close $fh; | |
143 my $seqio = Bio::SeqIO->new(-file=>$filename,-format=>'bsml'); | |
144 unlink $filename; | |
145 $seqio; | |
146 } | |
147 | |
148 *get_Stream_by_id = \&get_Stream_by_batch; | |
149 | |
150 =head2 get_Seq_by_acc | |
151 | |
152 Title : get_Seq_by_acc | |
153 Usage : $seq = $db->get_Seq_by_acc('X77802'); | |
154 Function: Gets a Bio::Seq object by accession number | |
155 Returns : A Bio::Seq object | |
156 Args : accession number (as a string) | |
157 Throws : "acc does not exist" exception | |
158 | |
159 | |
160 =cut | |
161 | |
162 sub get_Seq_by_acc{ | |
163 my ($self,@args) = @_; | |
164 return $self->get_Seq_by_id(@args); | |
165 } | |
166 | |
167 =head2 get_Seq_by_version | |
168 | |
169 Title : get_Seq_by_version | |
170 Usage : $seq = $db->get_Seq_by_version('X77802.1'); | |
171 Function: Gets a Bio::Seq object by sequence version | |
172 Returns : A Bio::Seq object | |
173 Args : accession.version (as a string) | |
174 Throws : "acc.version does not exist" exception | |
175 | |
176 =cut | |
177 | |
178 sub get_Seq_by_version{ | |
179 my ($self,@args) = @_; | |
180 return $self->get_Seq_by_id(@args); | |
181 } | |
182 | |
183 | |
184 1; |