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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.

Implemented Interfaces
       This class implementes the following interfaces.

       Bio::Seq::RichSeqI
	   Note that this includes implementing Bio::PrimarySeqI and
	   Bio::SeqI.

       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:

	 http://bugzilla.open-bio.org/

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)

   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 v5.14.1			  2011-07-22		  Bio::Seq::RichSeq(3)
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