Bio::Seq - Sequence object, with features
$seqio = Bio::SeqIO->new ( '-format' => 'Fasta' , -file => 'myfile.fasta'); $seqobj = $seqio->next_seq(); # features must implement Bio::SeqFeatureI @features = $seqobj->top_SeqFeatures(); # just top level @features = $seqobj->all_SeqFeatures(); # descend into sub features $seq = $seqobj->seq(); # actual sequence as a string $seqstr = $seqobj->subseq(10,50); $ann = $seqobj->annotation(); # annotation object
A Seq object is a sequence with sequence features placed on them. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface.
In bioperl we have 3 main players that people are going to use
Bio::PrimarySeq - just the sequence and its names, nothing else. Bio::SeqFeature - a location on a sequence, potentially with a sequence. and annotation Bio::Seq - A sequence and a collection of seqfeatures (an aggregate) with its own annotation.
Although bioperl is not tied to file formats heavily, these distrinctions do map to file formats sensibly and for some bioinformaticians this might help you:
Bio::PrimarySeq - Fasta file of a sequence Bio::SeqFeature - A single entry in an EMBL/GenBank/DDBJ feature table Bio::Seq - A single EMBL/GenBank/DDBJ entry
By having this split we avoid alot of nasty ciricular references (seqfeatures can hold a reference to a sequence without the sequence holding a reference to the seqfeature).
Ian Korf really helped in the design of the Seq and SeqFeature system.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
The primaryseq interface is the basic sequence getting and setting methods found on all sequences.
These methods implement the PrimarySeq interface by delegating to the primary_seq inside the object. This means that you can use a Seq object wherever there is a PrimarySeq, and of course, you are free to use these functions anyway.
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 : desc Usage : $seqobj->desc() Function: Sets/Gets the description of the sequnce Example : Returns : Args :
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 natural id, this method should return a stringified memory location. Also notice that this method is B<not> delegated to the internal PrimarySeq object 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
These methods are inherieted from the PrimarySeq interface and work as one expects, building new Bio::Seq objects or other information as expected.
Sequence Features are not transfered to the new objects. This is possibly a mistake. Anyone who feels the urge in dealing with this is welcome to give it a go.
Title : revcom Usage : $rev = $seq->revcom() Function: Produces a new Bio::Seq 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::Seq object Args : none
Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Example : Returns : a fresh Bio::Seq object Args :
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 : type Usage : Function: Example : Returns : Args :
These methods are specific to the Bio::Seq object, and not found on the Bio::PrimarySeq object
Title : seq Usage : $obj->primary_seq($newval) Function: Example : Returns : value of primary_seq Args : newvalue (optional)
Title : annotation Usage : $obj->annotation($seq_obj) Function: Example : Returns : value of annotation Args : newvalue (optional)
Title : add_SeqFeature Usage : $annseq->add_SeqFeature($feat); Function: Adds t Example : Returns : Args :
Title : top_SeqFeatures Usage : Function: Example : Returns : Args :
Title : all_SeqFeatures Usage : Function: Example : Returns : Args :
Title : fetch_SeqFeatures Usage : Function: Example : Returns : Args :
Title : species Usage : Function: Gets or sets the species Example : $species = $self->species(); Returns : Bio::Species object Args : Bio::Species object or none;
These methods are here to support the EMBL/GenBank/DDBJ format. The problem is that these formats require a certain amount of additional information (eg, what division they are from), but to make bioperl slavishly involved with this is just a bad idea.
If you want to use these methods, please preface them with a $as->can('method-name'). If this fails, then do something sensible. This means that we do not have to think about being in lock-step with EMBL/GenBank/DDBJ but can still support all the information that is required.
Title : division Usage : $obj->division($newval) Function: Returns : value of division Args : newvalue (optional)
Title : molecule Usage : $obj->molecule($newval) Function: Returns : type of molecule (DNA, mRNA) Args : newvalue (optional)
Title : add_date Usage : $self->add_domment($ref) Function: adds a date Example : Returns : Args :
Title : each_date Usage : foreach $dt ( $self->each_date() ) Function: gets an array of dates Example : Returns : Args :
Title : accession Usage : $obj->accession($newval) Function: Whilst the underlying sequence object does not have an accession, so we need one here. Wont stay when we do the reimplementation. Example : Returns : value of accession Args : newvalue (optional)
Title : add_secondary_accession Usage : $self->add_domment($ref) Function: adds a secondary_accession Example : Returns : Args :
Title : each_secondary_accession Usage : foreach $dt ( $self->each_secondary_accession() ) Function: gets an array of secondary_accessions Example : Returns : Args :
Title : sv Usage : $obj->sv($newval) Function: Returns : value of sv Args : newvalue (optional)
Title : keywords Usage : $obj->keywords($newval) Function: Returns : value of keywords Args : newvalue (optional)
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.