Bio::Seq(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

🌸 Bio::Seq 🌸

okay bestie, sit down, hydrate, because this is the sequence object in Bioperl and it's giving main character energy 💅. This page is from the User Contributed Perl Documentation and it's Bio::Seq(3pm) — aka the whole reason half your scripts exist. no cap.

✨ NAME ✨

Bio::Seq — Sequence object, with features 🧬🎀

✨ SYNOPSIS ✨

okay so this is literally the greatest hits of Bioperl, all in one place:

# 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," [",$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 transferred

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();

like, the chaining at the bottom? $seqobj->trunc(100,200)->revcom->translate() — that's not a function call, that's a lewk 💅 obsessed.

💖 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 it also implements its interface. it's giving "I contain multitudes" ✨

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 feature on a sequence, potentially with a sequence and a location 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 entry

By 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? the drama was avoided. growth 🌱. Check out Bio::PrimarySeq and Bio::SeqFeatureI for more information.

Ian Korf really helped in the design of the Seq and SeqFeature system. shoutout king 👑

🦋 Examples 🦋

A simple and fundamental block of code, the little starter pack fr fr:

use Bio::SeqIO;

my $seqIOobj = Bio::SeqIO->new(-file=>"1.fa"); # create a SeqIO object
my $seqobj = $seqIOobj->next_seq;              # get a Seq object

With 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. so it's reading, reversing, writing AND snooping. multitasking icon 😌

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, bestie, because it's lowkey a whole education. 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. ⚠️ yes, the > matters, that's the whole vibe check.

Using the

'-argument' => value

syntax 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. so many formats. they ate. 🍽️

$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. one method, two jobs, versatile queen 👑

$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->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 sequence

Some 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. like it just knows where everything lives. memory of an elephant, honestly 🐘

# 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
🫶 heads up bestie: those three methods hand you back brand new Seq objects — but the features do not come with them. no features transferred. don't say I didn't warn you.

Okay so you can also check if a string is even allowed in your sequence, and there's a whole lil ecosystem of objects hanging off your Seq. Let's go 💖

# 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();

Head to Bio::Species if you wanna know more about that object, bestie.

# the following method returns or accepts an Annotation object
# which in turn allows access to Annotation::Reference
# and Annotation::Comment objects:

$seqobj->annotation();

✨ Key thing: these annotations are usually about the entire sequence, unlike features (which are about specific spots). Details live in Bio::AnnotationCollectionI, Bio::Annotation::Collection, Bio::Annotation::Reference, and Bio::Annotation::Comment.

🧬 describing parts of a sequence (a.k.a. features)

You also gotta be able to describe defined portions of a sequence, right? The combo of some description + the matching sub-sequence is called a feature — an exon and its coordinates within a gene is one example, or a domain within a protein. Very main character.

# 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_count

Here's just some of what you can do with 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 sequence

Bio::PrimarySeq has the whole tea on PrimarySeq objects, iykyk.

# 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

# sub features. For complex join() statements, the feature
# is one sequence feature with many sub SeqFeatures

$feat->sub_SeqFeature  # returns array of sub seq features

For more on sequence features, go read Bio::SeqFeatureI and Bio::SeqFeature::Generic. 💅

Oh and also worth mentioning — you can grab a feature's start and end positions using a Bio::LocationI object:

$location = $feat->location # $location is a Bio::LocationI object
$location->start;           # start position
$location->end;             # end position

Why is that useful? Because you literally need a Bio::Location::SplitLocationI object to get at the coordinates buried inside Genbank or EMBL join() statements (like "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";
  }
}

More info lives in Bio::LocationI and Bio::Location::SplitLocationI. 🌸

✨ Implemented Interfaces ✨

This class implements the following interfaces. No cap.

  • Bio::SeqI — heads up, this includes implementing Bio::PrimarySeqI too.
  • 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. Fr fr, we love to see it. 🫶

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Why? Because many experienced and responsive experts will be able to 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.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney, inspired by Ian Korf objects

Email birney@ebi.ac.uk

CONTRIBUTORS

Jason Stajich E<lt>jason@bioperl.orgE<gt>
Mark A. Jensen maj -at- fortinbras -dot- us

📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. (iykyk, that underscore is the "don't touch unless you know what you're doing" flag 🙈)

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 object

PrimarySeq 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. What that means for you: you can use a Seq object wherever there's a PrimarySeq, and of course you're free to use these functions anyway. Slay.

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 parameter style with -seq and -alphabet being the names.

validate_seq

  • Title: validate_seq
  • Usage:
if(! $seqobj->validate_seq($seq_str) ) {
       print "sequence $seq_str is not valid for an object of
       alphabet ",$seqobj->alphabet, "\n";
  }
  • Function: Test that the given sequence is valid, i.e. contains only valid characters. The allowed characters are all letters (A-Z) and '-','.', '*','?','=' and '~'. Spaces are not valid. Note that this implementation does not take alphabet() into account.
  • Returns: 1 if the supplied sequence string is valid, 0 otherwise.
  • Args:
    • Sequence string to be validated
    • Boolean to throw an error if the sequence is invalid

length

  • Title: length
  • Usage: $len = $seq->length()
  • Function:
  • Example:
  • Returns: Integer representing the length of the sequence.
  • Args: None

✨ Methods 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 integers

🆔 display_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 id

🔑 accession_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 implementation, 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 number

📝 desc

  • Title: desc
  • Usage: $seqobj->desc($string) or $seqobj->desc()
  • Function: Sets or gets the description of the sequence
  • Example: (none given)
  • Returns: The description
  • Args: The description or none

🪪 primary_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 (or unset to undef). [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 id, or undef to unset the primary id.

🆕 can_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: (none given)
  • Returns: 1 or 0
  • Args: None

🔤 alphabet

  • Title: alphabet
  • Usage: if ( $obj->alphabet eq 'dna' ) { /Do Something/ }
  • Function: Get/Set 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: optional string to set : 'dna' | 'rna' | 'protein'

⭕ is_circular

  • Title: is_circular
  • Usage: if( $obj->is_circular) { /Do Something/ }
  • Function: Returns true if the molecule is circular
  • Returns: Boolean value
  • Args: none

🆔 Methods 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 scalar

🔢 version

  • 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 number

🏛️ authority

  • 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 scalar

📛 namespace

  • 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 scalar

📛 Methods 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 assume 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 scalar

📝 description

  • 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 scalar

🗂️ Methods for implementing Bio::AnnotatableI 🗂️

📎 annotation

  • Title: annotation
  • Usage:
$ann = $seq->annotation or
$seq->annotation($ann)
  • Function: Gets or sets the annotation
  • Returns: Bio::AnnotationCollectionI object
  • Args: None or Bio::AnnotationCollectionI object
See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information

🧺 Methods for delegating Bio::AnnotationCollectionI 🧺

📥 get_Annotations()

  • Usage: my @annotations = $seq->get_Annotations('key')
  • Function: Retrieves all the Bio::AnnotationI objects for a specific key for this object
  • Returns: list of Bio::AnnotationI - empty if no objects stored for a key
  • Args: string which is key for annotations

➕ add_Annotation()

  • Usage:
$seq->add_Annotation('reference',$object);
$seq->add_Annotation($object,'Bio::MyInterface::DiseaseI');
$seq->add_Annotation($object);
$seq->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI');
  • Function: Adds an annotation for a specific key for this sequence object. If the key is omitted, the object to be added must provide a value via its tagname(). If the archetype is provided, this and future objects added under that tag have to comply with the archetype and will be rejected otherwise.
  • Returns: none
  • Args: annotation key ('disease', 'dblink', ...) object to store (must be Bio::AnnotationI compliant) [optional] object archetype to map future storage of object of these types to

🗑️ remove_Annotations()

  • Usage: $seq->remove_Annotations()
  • Function: Remove the annotations for the specified key from this sequence object
  • Returns: an list of Bio::AnnotationI compliant objects which were stored under the given key(s) for this sequence object
  • Args: the key(s) (tag name(s), one or more strings) for which to remove annotations (optional; if none given, flushes all annotations)

🔢 get_num_of_annotations()

  • Usage: my $count = $seq->get_num_of_annotations()
  • Alias: num_Annotations
  • Function: Returns the count of all annotations stored for this sequence object
  • Returns: integer
  • Args: none

💖 Methods to implement Bio::FeatureHolderI 💖

This includes methods for retrieving, adding, and removing features.

get_SeqFeatures 🌸

Title: get_SeqFeatures

Usage: (none listed, bestie)

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.

Specific features can be obtained by primary tag, specified in the argument.

Use get_all_SeqFeatures() if you want the feature tree flattened into one single array.

Example:

my @feats = $seq->get_SeqFeatures or
my @genefeats = $seq->get_SeqFeatures('gene')

Returns: an array of Bio::SeqFeatureI implementing objects

Args: [optional] string (feature tag)

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: None

feature_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: None

add_SeqFeature ➕

Title: add_SeqFeature

Usage: $seq->add_SeqFeature($feat);

Function: Adds the given feature object to the feature array of this sequence. The object passed is required to implement the Bio::SeqFeatureI interface.

The 'EXPAND' qualifier (see L<Bio::FeatureHolderI>) is supported, but has no effect,

Returns: 1 on success

Args: A Bio::SeqFeatureI implementing object.

remove_SeqFeatures 🗑️

Title: remove_SeqFeatures

Usage: $seq->remove_SeqFeatures();

Function: Removes all attached SeqFeatureI objects or those with the specified primary tag

Example:

my @gene_feats = $seq->remove_seqFeatures('gene') or
my @feats = $seq->remove_seqFeatures()

Returns: The array of Bio::SeqFeatureI objects removed from the sequence

Args: None, or a feature primary tag

🌈 Methods 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 transferred to the new objects. To reverse complement and include the features use Bio::SeqUtils::revcom_with_features.

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: None

trunc ✂️

Title: trunc

Usage: $subseq = $myseq->trunc(10,100);

Function: Provides a truncation of a sequence

Example: (nothing here, bestie — literally blank)

Returns: A fresh Seq object

Args: A Seq object

id 🆔

Title: id

Usage: $id = $seq->id()

Function: This is mapped on display_id

Returns: value of display_id()

Args: [optional] value to update display_id

👑 Seq 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: (blank, no cap)

Returns: PrimarySeq object

Args: None or PrimarySeq object

species 🦋

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> object

See Bio::Species for more information

and that's the whole Bio::Seq(3pm) vibe, bestie! this page is from Bio::Seq(3pm), dated 2021-08-15, and it ships with perl v5.32.1. go off, read some sequences, and stay iconic 💅✨

📦 where this page comes from