Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq
# 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 objects
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
These functions are the ones that a specific implementation must define.
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 scalar
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 :
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 : None
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 : None
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 : None
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 :
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 : none
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
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 : none
Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Example : Returns : a fresh Bio::PrimarySeqI implementing object Args :
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 1
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!
Title : id Usage : $id = $seq->id() Function: Example : Returns : Args :
Title : length Usage : $len = $seq->length() Function: Example : Returns : Args :
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.
Title : str Usage : Function: Example : Returns : Args :
Title : ary Usage : Function: Example : Returns : Args :
Title : getseq Usage : Function: Example : Returns : Args :
Title : setseq Usage : Function: Example : Returns : Args :
Title : type Usage : Function: Example : Returns : Args :
Title : seq_len Usage : Function: Example : Returns : Args :
Title : out_fasta Usage : Function: Example : Returns : Args : Too many people are going call this function for me not to put it in
Title : GCG_checksum Usage : $myseq->GCG_checksum; Function : returns a gcg checksum for the sequence Example : Returns : Argument : none
These are some private functions for the PrimarySeqI interface. You do not need to implement these functions
Title : _attempt_to_load_Seq Usage : Function: Example : Returns : Args :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.