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Bio::Seq::RichSeqI.3pm
Langue: en
Version: 2010-05-19 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databasesSYNOPSIS
@secondary = $richseq->get_secondary_accessions; $division = $richseq->division; $mol = $richseq->molecule; @dates = $richseq->get_dates; $seq_version = $richseq->seq_version; $pid = $richseq->pid; @keywords = $richseq->get_keywords;
DESCRIPTION
This interface extends the Bio::SeqI interface to give additional functionality to sequences with richer data sources, in particular from database sequences (EMBL, GenBank and Swissprot).FEEDBACK
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User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferablyto 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
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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.ukAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _get_secondary_accessions
Title : get_secondary_accessions Usage : Function: Get the secondary accessions for a sequence. An implementation that allows modification of this array property should provide the methods add_secondary_accession and remove_secondary_accessions, with obvious purpose. Example : Returns : an array of strings Args : none
division
Title : division Usage : Function: Get (and set, depending on the implementation) the divison for a sequence. Examples from GenBank are PLN (plants), PRI (primates), etc. Example : Returns : a string Args :
molecule
Title : molecule Usage : Function: Get (and set, depending on the implementation) the molecule type for the sequence. This is not necessarily the same as Bio::PrimarySeqI::alphabet(), because it is databank-specific. Example : Returns : a string Args :
pid
Title : pid Usage : Function: Get (and set, depending on the implementation) the PID property for the sequence. Example : Returns : a string Args :
get_dates
Title : get_dates Usage : Function: Get (and set, depending on the implementation) the dates the databank entry specified for the sequence An implementation that allows modification of this array property should provide the methods add_date and remove_dates, with obvious purpose. Example : Returns : an array of strings Args :
seq_version
Title : seq_version Usage : Function: Get (and set, depending on the implementation) the version string of the sequence. Example : Returns : a string Args :
get_keywords
Title : get_keywords Usage : $obj->get_keywords() Function: Get the keywords for this sequence object. An implementation that allows modification of this array property should provide the methods add_keyword and remove_keywords, with obvious purpose. Returns : an array of strings Args :
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