| Filename | /Users/ap13/perl5/lib/perl5/Bio/DB/SeqI.pm |
| Statements | Executed 5 statements in 150µs |
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| 1 | 1 | 1 | 14µs | 28µs | Bio::DB::SeqI::BEGIN@79 |
| 1 | 1 | 1 | 8µs | 392µs | Bio::DB::SeqI::BEGIN@81 |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::SeqI::get_PrimarySeq_stream |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::SeqI::get_Seq_by_primary_id |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::SeqI::get_all_primary_ids |
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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 | |||||
| 16 | Bio::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 | |||||
| 33 | Abstract interface for a sequence database | ||||
| 34 | |||||
| 35 | =head1 FEEDBACK | ||||
| 36 | |||||
| 37 | =head2 Mailing Lists | ||||
| 38 | |||||
| 39 | User feedback is an integral part of the evolution of this and other | ||||
| 40 | Bioperl modules. Send your comments and suggestions preferably to one | ||||
| 41 | of 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 | |||||
| 48 | Please direct usage questions or support issues to the mailing list: | ||||
| 49 | |||||
| 50 | I<bioperl-l@bioperl.org> | ||||
| 51 | |||||
| 52 | rather than to the module maintainer directly. Many experienced and | ||||
| 53 | reponsive experts will be able look at the problem and quickly | ||||
| 54 | address it. Please include a thorough description of the problem | ||||
| 55 | with code and data examples if at all possible. | ||||
| 56 | |||||
| 57 | =head2 Reporting Bugs | ||||
| 58 | |||||
| 59 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
| 60 | the bugs and their resolution. Bug reports can be submitted via the | ||||
| 61 | web: | ||||
| 62 | |||||
| 63 | https://github.com/bioperl/bioperl-live/issues | ||||
| 64 | |||||
| 65 | =head1 AUTHOR - Ewan Birney | ||||
| 66 | |||||
| 67 | Email birney@ebi.ac.uk | ||||
| 68 | |||||
| 69 | =head1 APPENDIX | ||||
| 70 | |||||
| 71 | The rest of the documentation details each of the object methods. Internal | ||||
| 72 | methods are usually preceded with a _ | ||||
| 73 | |||||
| 74 | =cut | ||||
| 75 | |||||
| 76 | |||||
| 77 | package Bio::DB::SeqI; | ||||
| 78 | |||||
| 79 | 2 | 29µs | 2 | 42µs | # spent 28µs (14+14) within Bio::DB::SeqI::BEGIN@79 which was called:
# once (14µs+14µs) by base::import at line 79 # spent 28µs making 1 call to Bio::DB::SeqI::BEGIN@79
# spent 14µs making 1 call to strict::import |
| 80 | |||||
| 81 | 2 | 119µs | 2 | 392µs | # spent 392µs (8+384) within Bio::DB::SeqI::BEGIN@81 which was called:
# once (8µs+384µs) by base::import at line 81 # 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 : $stream = get_PrimarySeq_stream | ||||
| 118 | Function: Makes a Bio::SeqIO compliant object | ||||
| 119 | which provides a single method, next_seq | ||||
| 120 | Returns : Bio::SeqIO | ||||
| 121 | Args : none | ||||
| 122 | |||||
| 123 | =cut | ||||
| 124 | |||||
| 125 | sub get_PrimarySeq_stream{ | ||||
| 126 | my ($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 = $seqdb->get_all_primary_ids() | ||||
| 135 | Function: gives an array of all the primary_ids of the | ||||
| 136 | sequence objects in the database. These | ||||
| 137 | may be ids (display style) or accession numbers | ||||
| 138 | or something else completely different - they | ||||
| 139 | *are not* meaningful outside of this database | ||||
| 140 | implementation. | ||||
| 141 | Example : | ||||
| 142 | Returns : an array of strings | ||||
| 143 | Args : none | ||||
| 144 | |||||
| 145 | =cut | ||||
| 146 | |||||
| 147 | sub get_all_primary_ids{ | ||||
| 148 | my ($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 $db->get_all_primary_ids. | ||||
| 159 | There is no other way to get (or guess) the primary_ids | ||||
| 160 | in a database. | ||||
| 161 | |||||
| 162 | The other possibility is to get Bio::PrimarySeqI objects | ||||
| 163 | via the get_PrimarySeq_stream and the primary_id field | ||||
| 164 | on these objects are specified as the ids to use here. | ||||
| 165 | Returns : A Bio::Seq object | ||||
| 166 | Args : accession number (as a string) | ||||
| 167 | Throws : "acc does not exist" exception | ||||
| 168 | |||||
| 169 | =cut | ||||
| 170 | |||||
| 171 | sub get_Seq_by_primary_id { | ||||
| 172 | my ($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 | |||||
| 178 | 1 | 2µs | 1; | ||
| 179 | |||||
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