NAME
Bio::Seq - Sequence object, with features
SYNOPSIS
# This is the main sequence object in Bioperl
# gets a sequence from a file
$seqio = Bio::SeqIO->new( '-format' => 'embl' , -file => 'myfile.dat');
$seqobj = $seqio->next_seq();
# SeqIO can both read and write sequences; see Bio::SeqIO
# for more information and examples
# get from database
$db = Bio::DB::GenBank->new();
$seqobj = $db->get_Seq_by_acc('X78121');
# make from strings in script
$seqobj = Bio::Seq->new( -display_id => 'my_id',
-seq => $sequence_as_string);
# gets sequence as a string from sequence object
$seqstr = $seqobj->seq(); # actual sequence as a string
$seqstr = $seqobj->subseq(10,50); # slice in biological coordinates
# retrieves information from the sequence
# features must implement Bio::SeqFeatureI interface
@features = $seqobj->get_SeqFeatures(); # just top level
foreach my $feat ( @features ) {
print "Feature ",$feat->primary_tag," starts ",$feat->start," ends ",
$feat->end," strand ",$feat->strand,"\n";
# features retain link to underlying sequence object
print "Feature sequence is ",$feat->seq->seq(),"\n"
}
# sequences may have a species
if( defined $seq->species ) {
print "Sequence is from ",$species->binomial_name," [",$species->common_name,"]\n";
}
# annotation objects are Bio::AnnotationCollectionI's
$ann = $seqobj->annotation(); # annotation object
# references is one type of annotations to get. Also get
# comment and dblink. Look at Bio::AnnotationCollection for
# more information
foreach my $ref ( $ann->get_Annotations('reference') ) {
print "Reference ",$ref->title,"\n";
}
# you can get truncations, translations and reverse complements, these
# all give back Bio::Seq objects themselves, though currently with no
# features transfered
my $trunc = $seqobj->trunc(100,200);
my $rev = $seqobj->revcom();
# there are many options to translate - check out the docs
my $trans = $seqobj->translate();
# these functions can be chained together
my $trans_trunc_rev = $seqobj->trunc(100,200)->revcom->translate();DESCRIPTION
A Seq object is a sequence with sequence features placed on it. 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 frequently
Bio::PrimarySeq - just the sequence and its names, nothing else.
Bio::SeqFeatureI - a location on a sequence, potentially with a sequence
and annotation.
Bio::Seq - A sequence and a collection of sequence features
(an aggregate) with its own annotation.Although Bioperl is not tied heavily to file formats these distinctions do map to file formats sensibly and for some bioinformaticians this might help
Bio::PrimarySeq - Fasta file of a sequence
Bio::SeqFeatureI - A single entry in an EMBL/GenBank/DDBJ feature table
Bio::Seq - A single EMBL/GenBank/DDBJ entryBy having this split we avoid a lot of nasty circular references (sequence features can hold a reference to a sequence without the sequence holding a reference to the sequence feature). See Bio::PrimarySeq and Bio::SeqFeatureI for more information.
Ian Korf really helped in the design of the Seq and SeqFeature system.
Examples
A simple and fundamental block of code:
use Bio::SeqIO;
my $seqIOobj = Bio::SeqIO->new(-file=>"1.fa"); # create a SeqIO object
my $seqobj = $seqIOobj->next_seq; # get a Seq objectWith the Seq object in hand one has access to a powerful set of Bioperl methods and related Bioperl objects. This next script will take a file of sequences in EMBL format and create a file of the reverse-complemented sequences in Fasta format using Seq objects. It also prints out details about the exons it finds as sequence features in Genbank Flat File format.
use Bio::Seq;
use Bio::SeqIO;
$seqin = Bio::SeqIO->new( -format => 'EMBL' , -file => 'myfile.dat');
$seqout= Bio::SeqIO->new( -format => 'Fasta', -file => '>output.fa');
while((my $seqobj = $seqin->next_seq())) {
print "Seen sequence ",$seqobj->display_id,", start of seq ",
substr($seqobj->seq,1,10),"\n";
if( $seqobj->alphabet eq 'dna') {
$rev = $seqobj->revcom;
$id = $seqobj->display_id();
$id = "$id.rev";
$rev->display_id($id);
$seqout->write_seq($rev);
}
foreach $feat ( $seqobj->get_SeqFeatures() ) {
if( $feat->primary_tag eq 'exon' ) {
print STDOUT "Location ",$feat->start,":",
$feat->end," GFF[",$feat->gff_string,"]\n";
}
}
}Let's examine the script. The lines below import the Bioperl modules. Seq is the main Bioperl sequence object and SeqIO is the Bioperl support for reading sequences from files and to files
use Bio::Seq;
use Bio::SeqIO;These two lines create two SeqIO streams: one for reading in sequences and one for outputting sequences:
$seqin = Bio::SeqIO->new( -format => 'EMBL' , -file => 'myfile.dat');
$seqout= Bio::SeqIO->new( -format => 'Fasta', -file => '>output.fa');Notice that in the "$seqout" case there is a greater-than sign, indicating the file is being opened for writing.
Using the
'-argument' => valuesyntax is common in Bioperl. The file argument is like an argument to open() . You can also pass in filehandles or FileHandle objects by using the -fh argument (see Bio::SeqIO documentation for details). Many formats in Bioperl are handled, including Fasta, EMBL, GenBank, Swissprot (swiss), PIR, and GCG.
$seqin = Bio::SeqIO->new( -format => 'EMBL' , -file => 'myfile.dat');
$seqout= Bio::SeqIO->new( -format => 'Fasta', -file => '>output.fa');This is the main loop which will loop progressively through sequences in a file, and each call to $seqio->next_seq() provides a new Seq object from the file:
while((my $seqobj = $seqio->next_seq())) {This print line below accesses fields in the Seq object directly. The $seqobj->display_id is the way to access the display_id attribute of the Seq object. The $seqobj->seq method gets the actual sequence out as string. Then you can do manipulation of this if you want to (there are however easy ways of doing truncation, reverse-complement and translation).
print "Seen sequence ",$seqobj->display_id,", start of seq ",
substr($seqobj->seq,1,10),"\n";Bioperl has to guess the alphabet of the sequence, being either 'dna', 'rna', or 'protein'. The alphabet attribute is one of these three possibilities.
if( $seqobj->alphabet eq 'dna') {The $seqobj->revcom method provides the reverse complement of the Seq object as another Seq object. Thus, the $rev variable is a reference to another Seq object. For example, one could repeat the above print line for this Seq object (putting $rev in place of $seqobj). In this case we are going to output the object into the file stream we built earlier on.
$rev = $seqobj->revcom;When we output it, we want the id of the outputted object to be changed to "$id.rev", ie, with .rev on the end of the name. The following lines retrieve the id of the sequence object, add .rev to this and then set the display_id of the rev sequence object to this. Notice that to set the display_id attribute you just need call the same method, display_id(), with the new value as an argument. Getting and setting values with the same method is common in Bioperl.
$id = $seqobj->display_id();
$id = "$id.rev";
$rev->display_id($id);The write_seq method on the SeqIO output object, $seqout, writes the $rev object to the filestream we built at the top of the script. The filestream knows that it is outputting in fasta format, and so it provides fasta output.
$seqout->write_seq($rev);This block of code loops over sequence features in the sequence object, trying to find ones who have been tagged as 'exon'. Features have start and end attributes and can be outputted in Genbank Flat File format, GFF, a standarized format for sequence features.
foreach $feat ( $seqobj->get_SeqFeatures() ) {
if( $feat->primary_tag eq 'exon' ) {
print STDOUT "Location ",$feat->start,":",
$feat->end," GFF[",$feat->gff_string,"]\n";
}
}The code above shows how a few Bio::Seq methods suffice to read, parse, reformat and analyze sequences from a file. A full list of methods available to Bio::Seq objects is shown below. Bear in mind that some of these methods come from PrimarySeq objects, which are simpler than Seq objects, stripped of features (see Bio::PrimarySeq for more information).
# these methods return strings, and accept strings in some cases:
$seqobj->seq(); # string of sequence
$seqobj->subseq(5,10); # part of the sequence as a string
$seqobj->accession_number(); # when there, the accession number
$seqobj->alphabet(); # one of 'dna','rna',or 'protein'
$seqobj->seq_version() # when there, the version
$seqobj->keywords(); # when there, the Keywords line
$seqobj->length() # length
$seqobj->desc(); # description
$seqobj->primary_id(); # a unique id for this sequence regardless
# of its display_id or accession number
$seqobj->display_id(); # the human readable id of the sequenceSome of these values map to fields in common formats. For example, The display_id() method returns the LOCUS name of a Genbank entry, the (\S+) following the > character in a Fasta file, the ID from a SwissProt file, and so on. The desc() method will return the DEFINITION line of a Genbank file, the description following the display_id in a Fasta file, and the DE field in a SwissProt file.
# the following methods return new Seq objects, but
# do not transfer features across to the new object:
$seqobj->trunc(5,10) # truncation from 5 to 10 as new object
$seqobj->revcom # reverse complements sequence
$seqobj->translate # translation of the sequence
# if new() can be called this method returns 1, else 0
$seqobj->can_call_new
# the following method determines if the given string will be accepted
# by the seq() method - if the string is acceptable then validate()
# returns 1, or 0 if not
$seqobj->validate_seq($string)
# the following method returns or accepts a Species object:
$seqobj->species();Please see Bio::Species for more information on this object.
# the following method returns or accepts an Annotation object
# which in turn allows access to Annotation::Reference
# and Annotation::Comment objects:
$seqobj->annotation();These annotations typically refer to entire sequences, unlike features. See Bio::AnnotationCollectionI, Bio::Annotation::Collection, Bio::Annotation::Reference, and Bio::Annotation::Comment for details.
It is also important to be able to describe defined portions of a sequence. The combination of some description and the corresponding sub-sequence is called a feature - an exon and its coordinates within a gene is an example of a feature, or a domain within a protein.
# the following methods return an array of SeqFeatureI objects:
$seqobj->get_SeqFeatures # The 'top level' sequence features
$seqobj->get_all_SeqFeatures # All sequence features, including sub-seq
# features, such as features in an exon
# to find out the number of features use:
$seqobj->feature_countHere are just some of the methods available to SeqFeatureI objects:
# these methods return numbers:
$feat->start # start position (1 is the first base)
$feat->end # end position (2 is the second base)
$feat->strand # 1 means forward, -1 reverse, 0 not relevant
# these methods return or accept strings:
$feat->primary_tag # the name of the sequence feature, eg
# 'exon', 'glycoslyation site', 'TM domain'
$feat->source_tag # where the feature comes from, eg, 'EMBL_GenBank',
# or 'BLAST'
# this method returns the more austere PrimarySeq object, not a
# Seq object - the main difference is that PrimarySeq objects do not
# themselves contain sequence features
$feat->seq # the sequence between start,end on the
# correct strand of the sequenceSee Bio::PrimarySeq for more details on PrimarySeq objects.
# useful methods for feature comparisons, for start/end points
$feat->overlaps($other) # do $feat and $other overlap?
$feat->contains($other) # is $other completely within $feat?
$feat->equals($other) # do $feat and $other completely agree?
# one can also add features
$seqobj->add_SeqFeature($feat) # returns 1 if successful
$seqobj->add_SeqFeature(@features) # returns 1 if successful
# sub features. For complex join() statements, the feature
# is one sequence feature with many sub SeqFeatures
$feat->sub_SeqFeature # returns array of sub seq featuresPlease see Bio::SeqFeatureI and Bio::SeqFeature::Generic, for more information on sequence features.
It is worth mentioning that one can also retrieve the start and end positions of a feature using a Bio::LocationI object:
$location = $feat->location # $location is a Bio::LocationI object
$location->start; # start position
$location->end; # end positionThis is useful because one needs a Bio::Location::SplitLocationI object in order to retrieve the coordinates inside the Genbank or EMBL join() statements (e.g. "CDS join(51..142,273..495,1346..1474)"):
if ( $feat->location->isa('Bio::Location::SplitLocationI') &&
$feat->primary_tag eq 'CDS' ) {
foreach $loc ( $feat->location->sub_Location ) {
print $loc->start . ".." . $loc->end . "\n";
}
}See Bio::LocationI and Bio::Location::SplitLocationI for more information.
Implemented Interfaces
This class implements the following interfaces.
- Bio::SeqI
-
Note that this includes implementing Bio::PrimarySeqI.
- Bio::IdentifiableI
- Bio::DescribableI
- Bio::AnnotatableI
- Bio::FeatureHolderI
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.
bioperl-l@bioperl.org - General 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@bioperl.org
http://bugzilla.bioperl.org/AUTHOR - Ewan Birney, inspired by Ian Korf objects
Email birney@ebi.ac.uk
CONTRIBUTORS
Jason Stajich <jason@bioperl.org>
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".
new
Title : new
Usage : $seq = Bio::Seq->new( -seq => 'ATGGGGGTGGTGGTACCCT',
-id => 'human_id',
-accession_number => 'AL000012',
);
Function: Returns a new Seq object from
basic constructors, being a string for the sequence
and strings for id and accession_number
Returns : a new Bio::Seq objectPrimarySeq interface
The PrimarySeq interface provides the basic sequence getting and setting methods for on all sequences.
These methods implement the Bio::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.
seq
Title : seq
Usage : $string = $obj->seq()
Function: Get/Set 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
Args : Optionally on set the new value (a string). An optional second
argument presets the alphabet (otherwise it will be guessed).
Both parameters may also be given in named paramater style
with -seq and -alphabet being the names.validate_seq
Title : validate_seq
Usage : if(! $seq->validate_seq($seq_str) ) {
print "sequence $seq_str is not valid for an object of type ",
ref($seq), "\n";
}
Function: Validates a given sequence string. A validating sequence string
must be accepted by seq(). A string that does not validate will
lead to an exception if passed to seq().
The implementation provided here does not take alphabet() into
account. Allowed are all letters (A-Z) and '-','.', and '*'.
Example :
Returns : 1 if the supplied sequence string is valid for the object, and
0 otherwise.
Args : The sequence string to be validated.length
Title : length
Usage : $len = $seq->length()
Function:
Example :
Returns : Integer representing the length of the sequence.
Args : NoneMethods from the Bio::PrimarySeqI interface
subseq
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 : 2 integersdisplay_id
Title : display_id
Usage : $id = $obj->display_id or $obj->display_id($newid);
Function: Gets or sets the display id, also known as the common name of
the Seq 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 LOCUS
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/convenience issues.
Returns : A string
Args : None or a new idaccession_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".
Can also be used to set the accession number.
Example : $key = $seq->accession_number or $seq->accession_number($key)
Returns : A string
Args : None or an accession numberdesc
Title : desc
Usage : $seqobj->desc($string) or $seqobj->desc()
Function: Sets or gets the description of the sequence
Example :
Returns : The description
Args : The description or 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 implementation 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.
Can also be used to set the primary_id.
Also notice that this method is not delegated to the
internal Bio::PrimarySeq object
[Note this method name is likely to change in 1.3]
Example : $id = $seq->primary_id or $seq->primary_id($id)
Returns : A string
Args : None or an idcan_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
-alphabet => 'dna',
);
Example :
Returns : 1 or 0
Args : Nonealphabet
Title : alphabet
Usage : if ( $obj->alphabet 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 : Noneis_circular
Title : is_circular
Usage : if( $obj->is_circular) { /Do Something/ }
Function: Returns true if the molecule is circular
Returns : Boolean value
Args : noneMethods for Bio::IdentifiableI compliance
object_id
Title : object_id
Usage : $string = $obj->object_id()
Function: a string which represents the stable primary identifier
in this namespace of this object. For DNA sequences this
is its accession_number, similarly for protein sequences
This is aliased to accession_number().
Returns : A scalarversion
Title : version
Usage : $version = $obj->version()
Function: a number which differentiates between versions of
the same object. Higher numbers are considered to be
later and more relevant, but a single object described
the same identifier should represent the same concept
Returns : A numberauthority
Title : authority
Usage : $authority = $obj->authority()
Function: a string which represents the organisation which
granted the namespace, written as the DNS name for
organisation (eg, wormbase.org)
Returns : A scalarnamespace
Title : namespace
Usage : $string = $obj->namespace()
Function: A string representing the name space this identifier
is valid in, often the database name or the name
describing the collection
Returns : A scalarMethods for Bio::DescribableI compliance
display_name
Title : display_name
Usage : $string = $obj->display_name()
Function: A string which is what should be displayed to the user
the string should have no spaces (ideally, though a cautious
user of this interface would not assumme this) and should be
less than thirty characters (though again, double checking
this is a good idea)
This is aliased to display_id().
Returns : A scalardescription
Title : description
Usage : $string = $obj->description()
Function: A text string suitable for displaying to the user a
description. This string is likely to have spaces, but
should not have any newlines or formatting - just plain
text. The string should not be greater than 255 characters
and clients can feel justified at truncating strings at 255
characters for the purposes of display
This is aliased to desc().
Returns : A scalarMethods for implementing Bio::AnnotatableI
annotation
Title : annotation
Usage : $ann = $seq->annotation or $seq->annotation($annotation)
Function: Gets or sets the annotation
Returns : L<Bio::AnnotationCollectionI> object
Args : None or L<Bio::AnnotationCollectionI> objectSee Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information
Methods to implement Bio::FeatureHolderI
This includes methods for retrieving, adding, and removing features.
get_SeqFeatures
Title : get_SeqFeatures
Usage :
Function: Get the feature objects held by this feature holder.
Features which are not top-level are subfeatures of one or
more of the returned feature objects, which means that you
must traverse the subfeature arrays of each top-level
feature object in order to traverse all features associated
with this sequence.
Use get_all_SeqFeatures() if you want the feature tree
flattened into one single array.
Example :
Returns : an array of Bio::SeqFeatureI implementing objects
Args : noneAt some day we may want to expand this method to allow for a feature filter to be passed in.
get_all_SeqFeatures
Title : get_all_SeqFeatures
Usage : @feat_ary = $seq->get_all_SeqFeatures();
Function: Returns the tree of feature objects attached to this
sequence object flattened into one single array. Top-level
features will still contain their subfeature-arrays, which
means that you will encounter subfeatures twice if you
traverse the subfeature tree of the returned objects.
Use get_SeqFeatures() if you want the array to contain only
the top-level features.
Returns : An array of Bio::SeqFeatureI implementing objects.
Args : Nonefeature_count
Title : feature_count
Usage : $seq->feature_count()
Function: Return the number of SeqFeatures attached to a sequence
Returns : integer representing the number of SeqFeatures
Args : Noneadd_SeqFeature
Title : add_SeqFeature
Usage : $seq->add_SeqFeature($feat);
$seq->add_SeqFeature(@feat);
Function: Adds the given feature object (or each of an array of feature
objects to the feature array of this
sequence. The object passed is required to implement the
Bio::SeqFeatureI interface.
Returns : 1 on success
Args : A Bio::SeqFeatureI implementing object, or an array of such objects.remove_SeqFeatures
Title : remove_SeqFeatures
Usage : $seq->remove_SeqFeatures();
Function: Flushes all attached SeqFeatureI objects.
To remove individual feature objects, delete those from the returned
array and re-add the rest.
Example :
Returns : The array of Bio::SeqFeatureI objects removed from this seq.
Args : NoneMethods provided in the Bio::PrimarySeqI interface
These methods are inherited from the PrimarySeq interface and work as one expects, building new Bio::Seq objects or other information as expected. See Bio::PrimarySeq for more information.
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.
revcom
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 original sequence, and the
accession number is also identical. If someone wants to track
that this sequence has be reversed, it needs to define its own
extensions
To do an in-place 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
in-place edit.
Returns : A new (fresh) Bio::Seq object
Args : Nonetrunc
Title : trunc
Usage : $subseq = $myseq->trunc(10,100);
Function: Provides a truncation of a sequence
Example :
Returns : A fresh Seq object
Args : A Seq objectid
Title : id
Usage : $id = $seq->id()
Function: This is mapped on display_id
Returns : value of display_id()
Args : [optional] value to update display_idSeq only methods
These methods are specific to the Bio::Seq object, and not found on the Bio::PrimarySeq object
primary_seq
Title : primary_seq
Usage : $seq->primary_seq or $seq->primary_seq($newval)
Function: Get or set a PrimarySeq object
Example :
Returns : PrimarySeq object
Args : None or PrimarySeq objectspecies
Title : species
Usage : $species = $seq->species() or $seq->species($species)
Function: Gets or sets the species
Returns : L<Bio::Species> object
Args : None or L<Bio::Species> objectSee Bio::Species for more information