Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::Seq::RichSeq(3)  User Contributed Perl Documentation Bio::Seq::RichSeq(3)

NAME
       Bio::Seq::RichSeq - Module implementing a sequence created from a rich
       sequence	database entry

SYNOPSIS
       See Bio::Seq::RichSeqI and documentation	of methods.

DESCRIPTION
       This module implements Bio::Seq::RichSeqI, an interface for sequences
       created from or created for entries from/of rich	sequence databanks,
       like EMBL, GenBank, and SwissProt. Methods added	to the Bio::SeqI
       interface therefore focus on databank-specific information. Note	that
       not every rich databank format may use all of the properties provided.

       For more	information, please see	the relevant

Implemented Interfaces
       This class implementes the following interfaces.

       Bio::Seq::RichSeqI
	   Note	that this includes implementing	Bio::PrimarySeqI and
	   Bio::SeqI, specifically via Bio::Seq	and Bio::PrimarySeq. Please
	   review the documentation for	those modules on implementation
	   details relevant to those interfaces, as well as the	ones below.

       Bio::IdentifiableI
       Bio::DescribableI
       Bio::AnnotatableI

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	: $seq	  = Bio::Seq::RichSeq->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::RichSeq object

   division
	Title	: division
	Usage	: $obj->division($newval)
	Function:
	Returns	: value	of division
	Args	: newvalue (optional)

   molecule
	Title	: molecule
	Usage	: $obj->molecule($newval)
	Function:
	Returns	: type of molecule (DNA, mRNA)
	Args	: newvalue (optional)

   add_date
	Title	: add_date
	Usage	: $self->add_date($datestr)
	Function: adds one or more dates

		  This implementation stores dates as keyed annotation,	the
		  key being 'date_changed'. You	can take advantage of this
		  fact when accessing the annotation collection	directly.

	Example	:
	Returns	:
	Args	: a date string	or an array of such strings

   get_dates
	Title	: get_dates
	Usage	: my @dates = $seq->get_dates;
	Function: Get the dates	of the sequence	(usually, when it was created and
		  changed.
	Returns	: an array of date strings
	Args	:

   pid
	Title	: pid
	Usage	: my $pid = $seq->pid();
	Function: Get (and set,	depending on the implementation) the PID property
		  for the sequence.
	Returns	: a string
	Args	:

   accession
	Title	: accession
	Usage	: $obj->accession($newval)
	Function: Whilst the underlying	sequence object	does not
		  have an accession, so	we need	one here.

		  In this implementation this is merely	a synonym for
		  accession_number().
	Example	:
	Returns	: value	of accession
	Args	: newvalue (optional)

   add_secondary_accession
	Title	: add_secondary_accession
	Usage	: $self->add_domment($ref)
	Function: adds a secondary_accession

		  This implementation stores secondary accession numbers as
		  keyed	annotation, the	key being 'secondary_accession'. You
		  can take advantage of	this fact when accessing the
		  annotation collection	directly.

	Example	:
	Returns	:
	Args	: a string or an array of strings

   get_secondary_accessions
	Title	: get_secondary_accessions
	Usage	: my @acc = $seq->get_secondary_accessions();
	Function: Get the secondary accession numbers as strings.
	Returns	: An array of strings
	Args	: none

   seq_version
	Title	: seq_version
	Usage	: $obj->seq_version($newval)
	Function: Get/set the sequence version
	Returns	: value	of seq_version (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)
	Note	: this differs from Bio::PrimarySeq version() in that this explicitly
		  refers to the	sequence record	version	one would find in a typical
		  sequence file.

   add_keyword
	Title	: add_keyword
	Usage	: $obj->add_keyword($newval)
	Function: Add a	new keyword to the annotation of the sequence.

		  This implementation stores keywords as keyed annotation,
		  the key being	'keyword'. You can take	advantage of this
		  fact when accessing the annotation collection	directly.

	Returns	:
	Args	: value	to be added (optional) (a string)

   get_keywords
	Title	: get_keywords
	Usage	: $obj->get_keywords($newval)
	Function: Get the keywords for this sequence as	an array of strings.
	Returns	: an array of strings
	Args	:

Private	methods	and synonyms for backward compatibility
   _add_annotation_value
	Title	: _add_annotation_value
	Usage	:
	Function: Adds a value to the annotation collection under the specified
		  key. Note that this is not a public method.
	Returns	:
	Args	: key (a string), value(s) (one	or more	scalars)

   _get_annotation_values
	Title	: _get_annotation_values
	Usage	:
	Function: Gets the values of a specific	annotation as identified by the
		  key from the annotation collection. Note that	this is	not a
		  public method.
	Example	:
	Returns	: an array of strings
	Args	: the key (a string)

perl v5.24.1			  2017-07-08		  Bio::Seq::RichSeq(3)

NAME | SYNOPSIS | DESCRIPTION | Implemented Interfaces | FEEDBACK | AUTHOR - Ewan Birney | APPENDIX | Private methods and synonyms for backward compatibility

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Seq::RichSeq&sektion=3&manpath=FreeBSD+12.0-RELEASE+and+Ports>

home | help