NAME
Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq
SYNOPSIS
# get a Bio::PrimarySeqI compliant object somehow
# to test this is a seq object
$obj->isa("Bio::PrimarySeqI") || $obj->throw("$obj does not implement the Bio::PrimarySeqI interface");
# accessors
$string = $obj->seq();
$substring = $obj->subseq(12,50);
$display = $obj->display_id(); # for human display
$id = $obj->primary_id(); # unique id for this object, implementation defined
$unique_key= $obj->accession_number();
# unique biological id
# object manipulation
eval {
$rev = $obj->revcom();
};
if( $@ ) {
$obj->throw("Could not reverse complement. Probably not DNA. Actual exception\n$@\n");
}
$trunc = $obj->trunc(12,50);
# $rev and $trunc are Bio::PrimaySeqI compliant objectsDESCRIPTION
This object defines an abstract interface to basic sequence information. PrimarySeq is an object just for the sequence and its name(s), nothing more. Seq is the larger object complete with features. There is a pure perl implementation of this in Bio::PrimaySeq. If you just want to use Bio::PrimaySeq objects, then please read that module first. This module defines the interface, and is of more interest to people who want to wrap their own Perl Objects/RDBs/FileSystems etc in way that they "are" bioperl sequence objects, even though it is not using Perl to store the sequence etc.
This interface defines what bioperl consideres necessary to "be" a sequence, without providing an implementation of this. (An implementation is provided in Bio::PrimaySeq). If you want to provide a Bio::PrimarySeq 'compliant' object which in fact wraps another object/database/out-of-perl experience, then this is the correct thing to wrap, generally by providing a wrapper class which would inheriet from your object and this Bio::PrimaySeqI interface. The wrapper class then would have methods lists in the "Implementation Specific Functions" which would provide these methods for your object.
FEEDBACK
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.
vsns-bcd-perl@lists.uni-bielefeld.de - General discussion
vsns-bcd-perl-guts@lists.uni-bielefeld.de - Technically-oriented discussion
http://bio.perl.org/MailList.html - About the mailing listsReporting 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 email or the web:
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/AUTHOR - Ewan Birney
Email birney@sanger.ac.uk
Describe contact details here
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Implementation Specific Functions
These functions are the ones that a specific implementation must define.
seq
Title : seq
Usage : $string = $obj->seq()
Function: Returns the sequence as a string of letters. The
case of the letters is left up to the implementer.
Suggested cases are upper case for proteins and lower case for
DNA sequence (IUPAC standard),
but implementations are suggested to keep an open mind about
case (some users... want mixed case!)
Returns : A scalarsubseq
Title : subseq
Usage : $substring = $obj->subseq(10,40);
Function: returns the subseq from start to end, where the first base
is 1 and the number is inclusive, ie 1-2 are the first two
bases of the sequence
Start cannot be larger than end but can be equal
Returns : a string
Args :display_id
Title : display_id
Usage : $id_string = $obj->display_id();
Function: returns the display id, aka the common name of the Sequence object.
The semantics of this is that it is the most likely string
to be used as an identifier of the sequence, and likely to
have "human" readability. The id is equivalent to the ID
field of the GenBank/EMBL databanks and the id field of the
Swissprot/sptrembl database. In fasta format, the >(\S+) is
presumed to be the id, though some people overload the id
to embed other information. Bioperl does not use any
embedded information in the ID field, and people are
encouraged to use other mechanisms (accession field for
example, or extending the sequence object) to solve this.
Notice that $seq->id() maps to this function, mainly for
legacy/convience issues
Returns : A string
Args : Noneaccession_number
Title : accession_number
Usage : $unique_biological_key = $obj->accession_number;
Function: Returns the unique biological id for a sequence, commonly
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the
unique id for the implemetation, allowing multiple objects
to have the same accession number in a particular implementation.
For sequences with no accession number, this method should return
"unknown".
Returns : A string
Args : Noneprimary_id
Title : primary_id
Usage : $unique_implementation_key = $obj->primary_id;
Function: Returns the unique id for this object in this
implementation. This allows implementations to manage
their own object ids in a way the implementaiton can control
clients can expect one id to map to one object.
For sequences with no accession number, this method should return
a stringified memory location.
Returns : A string
Args : Nonecan_call_new
Title : can_call_new
Usage : if( $obj->can_call_new ) {
$newobj = $obj->new( %param );
}
Function: can_call_new returns 1 or 0 depending
on whether an implementation allows new
constructor to be called. If a new constructor
is allowed, then it should take the followed hashed
constructor list.
$myobject->new( -seq => $sequence_as_string,
-display_id => $id
-accession_number => $accession
-moltype => 'dna',
);
Example :
Returns : 1 or 0
Args :moltype
Title : moltype
Usage : if( $obj->moltype eq 'dna' ) { /Do Something/ }
Function: Returns the type of sequence being one of
'dna', 'rna' or 'protein'. This is case sensitive.
This is not called <type> because this would cause
upgrade problems from the 0.5 and earlier Seq objects.
Returns : a string either 'dna','rna','protein'. NB - the object must
make a call of the type - if there is no type specified it
has to guess.
Args : noneOptional Implementation Functions
The following functions rely on the above functions. A implementing class does not need to provide these functions, as they will be provided by this class, but is free to override these functions.
All these functions are type of object constructor, which use the $obj->can_call_new() to see whether the new object should be made with the current implementation. If this is not possible, then they attempt a run-time loading of the Bio::PrimarySeq class which is then used to make the new objects.
Implementors which really want to control how objects are created (eg, for object persistence over a database, or objects in a CORBA framework), they are encouraged to override these methods
revcom
Title : revcom
Usage : $rev = $seq->revcom()
Function: Produces a new Bio::PrimarySeqI implementing object which
is the reversed complement of the sequence. For protein
sequences this throws an exception of "Sequence is a protein. Cannot revcom"
The id is the same id as the orginal sequence, and the accession number
is also indentical. If someone wants to track that this sequence has be
reversed, it needs to define its own extensions
To do an inplace edit of an object you can go:
$seq = $seq->revcom();
This of course, causes Perl to handle the garbage collection of the old
object, but it is roughly speaking as efficient as an inplace edit.
Returns : A new (fresh) Bio::PrimarySeqI object
Args : nonetrunc
Title : trunc
Usage : $subseq = $myseq->trunc(10,100);
Function: Provides a truncation of a sequence,
Example :
Returns : a fresh Bio::PrimarySeqI implementing object
Args :translate
Title : translate
Usage : $protein_seq_obj = $dna_seq_obj->translate
Function:
Provides the translation of the DNA sequence
using full IUPAC ambiguities in DNA/RNA and amino acid codes.
The resulting translation is identical to EMBL/TREMBL database
translations.
Returns : A Bio::PrimarySeqI implementing object
Args : character for terminator (optional) defaults to '*'
character for unknown amino acid (optional) defaults to 'X'
frame (optional) valid values 0, 1, 3, defaults to 0
codon table id (optional) defaults to 1translate_old
Title : translate_old
Usage : $protein_seq_obj = $dna_seq_obj->translate_old
Function: Provides the translation of the DNA sequence
Returns : A Bio::PrimarySeqI implementing object
Args : character for unknown amino acid (optional),
frame (optional)
EB: this function is badly written and needs an overhaul
HL: delete this method when confident that the new translate works!id
Title : id
Usage : $id = $seq->id()
Function:
Example :
Returns :
Args :length
Title : length
Usage : $len = $seq->length()
Function:
Example :
Returns :
Args :Methods for Backward Compatibility
These methods are here for backward compatibility with the old, 0.5 Seq objects. They all throw warnings that someone is using a deprecated method, and may eventually be removed completely from this object. However, they are important to ease the transition from the old system.
str
Title : str
Usage :
Function:
Example :
Returns :
Args :ary
Title : ary
Usage :
Function:
Example :
Returns :
Args :getseq
Title : getseq
Usage :
Function:
Example :
Returns :
Args :setseq
Title : setseq
Usage :
Function:
Example :
Returns :
Args :type
Title : type
Usage :
Function:
Example :
Returns :
Args :seq_len
Title : seq_len
Usage :
Function:
Example :
Returns :
Args :out_fasta
Title : out_fasta
Usage :
Function:
Example :
Returns :
Args :
Too many people are going call this function for me not to put it in GCG_checksum
Title : GCG_checksum
Usage : $myseq->GCG_checksum;
Function : returns a gcg checksum for the sequence
Example :
Returns :
Argument : nonePrivate functions
These are some private functions for the PrimarySeqI interface. You do not need to implement these functions
_attempt_to_load_Seq
Title : _attempt_to_load_Seq
Usage :
Function:
Example :
Returns :
Args :