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BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::PrimarySeq

NAME

Bio::PrimarySeq - Bioperl lightweight sequence object

SYNOPSIS

# Bio::SeqIO for file reading, Bio::DB::GenBank for
# database reading

use Bio::Seq;
use Bio::SeqIO;
use Bio::DB::GenBank;

# make from memory

$seqobj = Bio::PrimarySeq->new (
    -seq              => 'ATGGGGTGGGCGGTGGGTGGTTTG',
    -id               => 'GeneFragment-12',
    -accession_number => 'X78121',
    -alphabet         => 'dna',
    -is_circular      => 1,
);
print "Sequence ", $seqobj->id(), " with accession ",
  $seqobj->accession_number, "\n";

# read from file

$inputstream = Bio::SeqIO->new(
    -file   => "myseq.fa",
    -format => 'Fasta',
);
$seqobj = $inputstream->next_seq();
print "Sequence ", $seqobj->id(), " and desc ", $seqobj->desc, "\n";

# to get out parts of the sequence.

print "Sequence ", $seqobj->id(), " with accession ",
  $seqobj->accession_number, " and desc ", $seqobj->desc, "\n";

$string  = $seqobj->seq();
$string2 = $seqobj->subseq(1,40);

DESCRIPTION

PrimarySeq is a lightweight sequence object, storing the sequence, its name, a computer-useful unique name, and other fundamental attributes. It does not contain sequence features or other information. To have a sequence with sequence features you should use the Seq object which uses this object.

Although new users will use Bio::PrimarySeq a lot, in general you will be using it from the Bio::Seq object. For more information on Bio::Seq see Bio::Seq. For interest you might like to know that Bio::Seq has-a Bio::PrimarySeq and forwards most of the function calls to do with sequence to it (the has-a relationship lets us get out of a otherwise nasty cyclical reference in Perl which would leak memory).

Sequence objects are defined by the Bio::PrimarySeqI interface, and this object is a pure Perl implementation of the interface. If that's gibberish to you, don't worry. The take home message is that this object is the bioperl default sequence object, but other people can use their own objects as sequences if they so wish. If you are interested in wrapping your own objects as compliant Bioperl sequence objects, then you should read the Bio::PrimarySeqI documentation

The documentation of this object is a merge of the Bio::PrimarySeq and Bio::PrimarySeqI documentation. This allows all the methods which you can call on sequence objects here.

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://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. Many experienced and reponsive experts will be able 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 the bugs and their resolution. Bug reports can be submitted via the web:

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

AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : $seqobj = Bio::PrimarySeq->new( -seq => 'ATGGGGGTGGTGGTACCCT',
                                          -id  => 'human_id',
                                          -accession_number => 'AL000012',
                                          );
Function: Returns a new primary seq object from
          basic constructors, being a string for the sequence
          and strings for id and accession_number.

          Note that you can provide an empty sequence string. However, in
          this case you MUST specify the type of sequence you wish to
          initialize by the parameter -alphabet. See alphabet() for possible
          values.
Returns : a new Bio::PrimarySeq object
Args    : -seq              => sequence string
          -ref_to_seq       => ... or reference to a sequence string
          -display_id       => display id of the sequence (locus name)
          -accession_number => accession number
          -primary_id       => primary id (Genbank id)
          -version          => version number
          -namespace        => the namespace for the accession
          -authority        => the authority for the namespace
          -description      => description text
          -desc             => alias for description
          -alphabet         => skip alphabet guess and set it to dna, rna or protein
          -id               => alias for display id
          -is_circular      => boolean to indicate that sequence is circular
          -direct           => boolean to directly set sequences. The next time -seq,
                               seq() or -ref_to_seq is use, the sequence will not be
                               validated. Be careful with this...
          -nowarnonempty    => boolean to avoid warning when sequence is empty

seq

Title   : seq
Usage   : $string = $seqobj->seq();
Function: Get or 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 you should not rely on this. An error is thrown if
          the sequence contains invalid characters: see validate_seq().
Returns : A scalar
Args    : - Optional new sequence value (a string) to set
          - Optional alphabet (it is guessed by default)

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 and that empty
          sequences are considered valid.
Returns : 1 if the supplied sequence string is valid, 0 otherwise.
Args    : - Sequence string to be validated
          - Boolean to optionally throw an error if the sequence is invalid

subseq

Title   : subseq
Usage   : $substring = $seqobj->subseq(10,40);
          $substring = $seqobj->subseq(10,40,'nogap');
          $substring = $seqobj->subseq(-start=>10, -end=>40, -replace_with=>'tga');
          $substring = $seqobj->subseq($location_obj);
          $substring = $seqobj->subseq($location_obj, -nogap => 1);
Function: Return the subseq from start to end, where the first sequence
          character has coordinate 1 number is inclusive, ie 1-2 are the
          first two characters of the sequence. The given start coordinate
          has to be larger than the end, even if the sequence is circular.
Returns : a string
Args    : integer for start position
          integer for end position
                OR
          Bio::LocationI location for subseq (strand honored)
          Specify -NOGAP=>1 to return subseq with gap characters removed
          Specify -REPLACE_WITH=>$new_subseq to replace the subseq returned
          with $new_subseq in the sequence object

length

Title   : length
Usage   : $len = $seqobj->length();
Function: Get the stored length of the sequence in number of symbols (bases
          or amino acids). In some circumstances, you can also set this attribute:

          1. For empty sequences, you can set the length to anything you want:
             my $seqobj = Bio::PrimarySeq->new( -length => 123 );
             my $len = $seqobj->len; # 123
          2. To save memory when using very long sequences, you can set the
             length of the sequence to the length of the sequence (and nothing
             else):
             my $seqobj = Bio::PrimarySeq->new( -seq => 'ACGT...' ); # 1 Mbp sequence
             # process $seqobj... then after you're done with it
             $seqobj->length($seqobj->length);
             $seqobj->seq(undef); # free memory!
             my $len = $seqobj->len; # 1 Mbp

          Note that if you set seq() to a value other than undef at any time,
          the length attribute will be reset.
Returns : integer representing the length of the sequence.
Args    : Optionally, the value on set

display_id

Title   : display_id or display_name
Usage   : $id_string = $seqobj->display_id();
Function: Get or set 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.

          With the new Bio::DescribeableI interface, display_name aliases
          to this method.
Returns : A string for the display ID
Args    : Optional string for the display ID to set

accession_number

Title   : accession_number or object_id
Usage   : $unique_key = $seqobj->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".

          [Note this method name is likely to change in 1.3]

          With the new Bio::IdentifiableI interface, this is aliased
          to object_id
Returns : A string
Args    : A string (optional) for setting

primary_id

Title   : primary_id
Usage   : $unique_key = $seqobj->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 primary id, this method
          should return a stringified memory location.
Returns : A string
Args    : A string (optional, for setting)

alphabet

Title   : alphabet
Usage   : if( $seqobj->alphabet eq 'dna' ) { # Do something }
Function: Get/set the alphabet of sequence, 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 alphabet specified it
          has to guess.
Args    : optional string to set : 'dna' | 'rna' | 'protein'

desc

Title   : desc or description
Usage   : $seqobj->desc($newval);
Function: Get/set description of the sequence.

          'description' is an alias for this for compliance with the
          Bio::DescribeableI interface.
Returns : value of desc (a string)
Args    : newvalue (a string or undef, optional)

can_call_new

Title   : can_call_new
Usage   :
Function:
Example :
Returns : true
Args    :

id

Title   : id
Usage   : $id = $seqobj->id();
Function: This is mapped on display_id
Example :
Returns :
Args    :

is_circular

Title   : is_circular
Usage   : if( $seqobj->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 = $seqobj->object_id();
Function: Get or set 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
Args    : Optional object ID to set.

version

Title   : version
Usage   : $version = $seqobj->version();
Function: Get or set 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
Args    : Optional version to set.

authority

Title   : authority
Usage   : $authority = $seqobj->authority();
Function: Get or set a string which represents the organisation which
          granted the namespace, written as the DNS name of the
          organisation (eg, wormbase.org).
Returns : A scalar
Args    : Optional authority to set.

namespace

Title   : namespace
Usage   : $string = $seqobj->namespace();
Function: Get or set a string representing the name space this identifier
          is valid in, often the database name or the name describing the
          collection.
Returns : A scalar
Args    : Optional namespace to set.

Methods for Bio::DescribableI compliance

This comprises of display_name and description.

display_name

Title   : display_name
Usage   : $string = $seqobj->display_name();
Function: Get or set 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 string for the display name
Args    : Optional string for the display name to set.

description

Title   : description
Usage   : $string = $seqobj->description();
Function: Get or set 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 string for the description
Args    : Optional string for the description to set.

Methods Inherited from Bio::PrimarySeqI

These methods are available on Bio::PrimarySeq, although they are actually implemented on Bio::PrimarySeqI

revcom

Title   : revcom
Usage   : $rev = $seqobj->revcom();
Function: Produces a new Bio::SeqI 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:

          $seqobj = $seqobj->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::SeqI object
Args    : none

trunc

Title   : trunc
Usage   : $subseq = $myseq->trunc(10,100);
Function: Provides a truncation of a sequence,
Returns : A fresh Bio::SeqI implementing object.
Args    : Numbers for the start and end positions

Internal methods

These are internal methods to PrimarySeq

_guess_alphabet

Title   : _guess_alphabet
Usage   :
Function: Automatically guess and set the type of sequence: dna, rna, protein
          or '' if the sequence was empty. This method first removes dots (.),
          dashes (-) and question marks (?) before guessing the alphabet
          using the IUPAC conventions for ambiguous residues. Since the DNA and
          RNA characters are also valid characters for proteins, there is
          no foolproof way of determining the right alphabet. This is our best
          guess only!
Returns : string 'dna', 'rna', 'protein' or ''.
Args    : none