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For bin/pan_genome_post_analysis
  Run on Fri Mar 27 11:43:32 2015
Reported on Fri Mar 27 11:46:12 2015

Filename/Users/ap13/perl5/lib/perl5/Bio/DB/SeqI.pm
StatementsExecuted 5 statements in 150µs
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11114µs28µsBio::DB::SeqI::::BEGIN@79Bio::DB::SeqI::BEGIN@79
1118µs392µsBio::DB::SeqI::::BEGIN@81Bio::DB::SeqI::BEGIN@81
0000s0sBio::DB::SeqI::::get_PrimarySeq_streamBio::DB::SeqI::get_PrimarySeq_stream
0000s0sBio::DB::SeqI::::get_Seq_by_primary_idBio::DB::SeqI::get_Seq_by_primary_id
0000s0sBio::DB::SeqI::::get_all_primary_idsBio::DB::SeqI::get_all_primary_ids
Call graph for these subroutines as a Graphviz dot language file.
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1#
2# BioPerl module for Bio::DB::SeqI.pm
3#
4# Please direct questions and support issues to <bioperl-l@bioperl.org>
5#
6# Cared for by Ewan Birney <birney@ebi.ac.uk>
7#
8# Copyright Ewan Birney
9#
10# You may distribute this module under the same terms as perl itself
11#
12
13
14=head1 NAME
15
16Bio::DB::SeqI - Abstract Interface for Sequence databases
17
18=head1 SYNOPSIS
19
20 # get a Bio::DB::SeqI somehow
21
22 $seq = $seqdb->get_Seq_by_id('some-id');
23 $seq = $seqdb->get_Seq_by_acc('some-accession-number');
24
25 @ids = $seqdb->get_all_ids();
26 $stream = $seqdb->get_PrimarySeq_stream();
27 while((my $seq = $stream->next_seq()) {
28 # $seq is a PrimarySeqI compliant object
29 }
30
31=head1 DESCRIPTION
32
33Abstract interface for a sequence database
34
35=head1 FEEDBACK
36
37=head2 Mailing Lists
38
39User feedback is an integral part of the evolution of this and other
40Bioperl modules. Send your comments and suggestions preferably to one
41of the Bioperl mailing lists. Your participation is much appreciated.
42
43 bioperl-l@bioperl.org - General discussion
44 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
45
46=head2 Support
47
48Please direct usage questions or support issues to the mailing list:
49
50I<bioperl-l@bioperl.org>
51
52rather than to the module maintainer directly. Many experienced and
53reponsive experts will be able look at the problem and quickly
54address it. Please include a thorough description of the problem
55with code and data examples if at all possible.
56
57=head2 Reporting Bugs
58
59Report bugs to the Bioperl bug tracking system to help us keep track
60the bugs and their resolution. Bug reports can be submitted via the
61web:
62
63 https://github.com/bioperl/bioperl-live/issues
64
65=head1 AUTHOR - Ewan Birney
66
67Email birney@ebi.ac.uk
68
69=head1 APPENDIX
70
71The rest of the documentation details each of the object methods. Internal
72methods are usually preceded with a _
73
74=cut
75
76
77package Bio::DB::SeqI;
78
79229µs242µs
# spent 28µs (14+14) within Bio::DB::SeqI::BEGIN@79 which was called: # once (14µs+14µs) by base::import at line 79
use strict;
# spent 28µs making 1 call to Bio::DB::SeqI::BEGIN@79 # spent 14µs making 1 call to strict::import
80
812119µs2392µs
# spent 392µs (8+384) within Bio::DB::SeqI::BEGIN@81 which was called: # once (8µs+384µs) by base::import at line 81
use base qw(Bio::DB::RandomAccessI);
# spent 392µs making 1 call to Bio::DB::SeqI::BEGIN@81 # spent 384µs making 1 call to base::import, recursion: max depth 2, sum of overlapping time 384µs
82
83=head1 Methods inherited from Bio::DB::RandomAccessI
84
85=head2 get_Seq_by_id
86
87 Title : get_Seq_by_id
88 Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
89 Function: Gets a Bio::Seq object by its name
90 Returns : a Bio::Seq object
91 Args : the id (as a string) of a sequence
92 Throws : "id does not exist" exception
93
94=head2 get_Seq_by_acc
95
96 Title : get_Seq_by_acc
97 Usage : $seq = $db->get_Seq_by_acc('X77802');
98 Function: Gets a Bio::Seq object by accession number
99 Returns : A Bio::Seq object
100 Args : accession number (as a string)
101 Throws : "acc does not exist" exception
102
103=head2 get_Seq_by_version
104
105 Title : get_Seq_by_version
106 Usage : $seq = $db->get_Seq_by_version('X77802.1');
107 Function: Gets a Bio::Seq object by sequence version
108 Returns : A Bio::Seq object
109 Args : accession.version (as a string)
110 Throws : "acc.version does not exist" exception
111
112=head1 Methods [that were] specific for Bio::DB::SeqI
113
114=head2 get_PrimarySeq_stream
115
116 Title : get_PrimarySeq_stream
117 Usage : $stream = get_PrimarySeq_stream
118 Function: Makes a Bio::SeqIO compliant object
119 which provides a single method, next_seq
120 Returns : Bio::SeqIO
121 Args : none
122
123=cut
124
125sub get_PrimarySeq_stream{
126 my ($self,@args) = @_;
127 $self->throw("Object did not provide a PrimarySeq stream object");
128}
129
130
131=head2 get_all_primary_ids
132
133 Title : get_all_ids
134 Usage : @ids = $seqdb->get_all_primary_ids()
135 Function: gives an array of all the primary_ids of the
136 sequence objects in the database. These
137 may be ids (display style) or accession numbers
138 or something else completely different - they
139 *are not* meaningful outside of this database
140 implementation.
141 Example :
142 Returns : an array of strings
143 Args : none
144
145=cut
146
147sub get_all_primary_ids{
148 my ($self,@args) = @_;
149 $self->throw("Object did not provide a get_all_ids method");
150}
151
152
153=head2 get_Seq_by_primary_id
154
155 Title : get_Seq_by_primary_id
156 Usage : $seq = $db->get_Seq_by_primary_id($primary_id_string);
157 Function: Gets a Bio::Seq object by the primary id. The primary
158 id in these cases has to come from $db->get_all_primary_ids.
159 There is no other way to get (or guess) the primary_ids
160 in a database.
161
162 The other possibility is to get Bio::PrimarySeqI objects
163 via the get_PrimarySeq_stream and the primary_id field
164 on these objects are specified as the ids to use here.
165 Returns : A Bio::Seq object
166 Args : accession number (as a string)
167 Throws : "acc does not exist" exception
168
169=cut
170
171sub get_Seq_by_primary_id {
172 my ($self,@args) = @_;
173 $self->throw("Abstract database call of get_Seq_by_primary_id. Your database".
174 " has not implemented this method!");
175
176}
177
17812µs1;
179
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