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.\" ========================================================================
.\"
.IX Title "Bio::DB::SeqI 3pm"
.TH Bio::DB::SeqI 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::DB::SeqI \- Abstract Interface for Sequence databases
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&   # get a Bio::DB::SeqI somehow
\&
\&   $seq = $seqdb\->get_Seq_by_id(\*(Aqsome\-id\*(Aq);
\&   $seq = $seqdb\->get_Seq_by_acc(\*(Aqsome\-accession\-number\*(Aq);
\&
\&   @ids = $seqdb\->get_all_ids();
\&   $stream = $seqdb\->get_PrimarySeq_stream();
\&   while((my $seq = $stream\->next_seq()) {
\&      # $seq is a PrimarySeqI compliant object
\&   }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Abstract interface for a sequence database
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Ewan Birney"
.IX Header "AUTHOR - Ewan Birney"
Email birney@ebi.ac.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
.SH "Methods inherited from Bio::DB::RandomAccessI"
.IX Header "Methods inherited from Bio::DB::RandomAccessI"
.SS "get_Seq_by_id"
.IX Subsection "get_Seq_by_id"
.Vb 6
\& Title   : get_Seq_by_id
\& Usage   : $seq = $db\->get_Seq_by_id(\*(AqROA1_HUMAN\*(Aq)
\& Function: Gets a Bio::Seq object by its name
\& Returns : a Bio::Seq object
\& Args    : the id (as a string) of a sequence
\& Throws  : "id does not exist" exception
.Ve
.SS "get_Seq_by_acc"
.IX Subsection "get_Seq_by_acc"
.Vb 6
\& Title   : get_Seq_by_acc
\& Usage   : $seq = $db\->get_Seq_by_acc(\*(AqX77802\*(Aq);
\& Function: Gets a Bio::Seq object by accession number
\& Returns : A Bio::Seq object
\& Args    : accession number (as a string)
\& Throws  : "acc does not exist" exception
.Ve
.SS "get_Seq_by_version"
.IX Subsection "get_Seq_by_version"
.Vb 6
\& Title   : get_Seq_by_version
\& Usage   : $seq = $db\->get_Seq_by_version(\*(AqX77802.1\*(Aq);
\& Function: Gets a Bio::Seq object by sequence version
\& Returns : A Bio::Seq object
\& Args    : accession.version (as a string)
\& Throws  : "acc.version does not exist" exception
.Ve
.SH "Methods [that were] specific for Bio::DB::SeqI"
.IX Header "Methods [that were] specific for Bio::DB::SeqI"
.SS "get_PrimarySeq_stream"
.IX Subsection "get_PrimarySeq_stream"
.Vb 6
\& Title   : get_PrimarySeq_stream
\& Usage   : $stream = get_PrimarySeq_stream
\& Function: Makes a Bio::SeqIO compliant object
\&           which provides a single method, next_seq
\& Returns : Bio::SeqIO
\& Args    : none
.Ve
.SS "get_all_primary_ids"
.IX Subsection "get_all_primary_ids"
.Vb 11
\& Title   : get_all_ids
\& Usage   : @ids = $seqdb\->get_all_primary_ids()
\& Function: gives an array of all the primary_ids of the 
\&           sequence objects in the database. These
\&           may be ids (display style) or accession numbers
\&           or something else completely different \- they
\&           *are not* meaningful outside of this database
\&           implementation.
\& Example :
\& Returns : an array of strings
\& Args    : none
.Ve
.SS "get_Seq_by_primary_id"
.IX Subsection "get_Seq_by_primary_id"
.Vb 6
\& Title   : get_Seq_by_primary_id
\& Usage   : $seq = $db\->get_Seq_by_primary_id($primary_id_string);
\& Function: Gets a Bio::Seq object by the primary id. The primary
\&           id in these cases has to come from $db\->get_all_primary_ids.
\&           There is no other way to get (or guess) the primary_ids
\&           in a database.
\&
\&           The other possibility is to get Bio::PrimarySeqI objects
\&           via the get_PrimarySeq_stream and the primary_id field
\&           on these objects are specified as the ids to use here.
\& Returns : A Bio::Seq object
\& Args    : accession number (as a string)
\& Throws  : "acc does not exist" exception
.Ve