Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::DB::SeqI.3pm

NAME

Bio::DB::SeqI - Abstract Interface for Sequence databases

SYNOPSIS

    # get a Bio::DB::SeqI somehow
 
    $seq = $seqdb->get_Seq_by_id('some-id');
    $seq = $seqdb->get_Seq_by_acc('some-accession-number');
 
    @ids = $seqdb->get_all_ids();
    $stream = $seqdb->get_PrimarySeq_stream();
    while((my $seq = $stream->next_seq()) {
       # $seq is a PrimarySeqI compliant object
    }
 
 

DESCRIPTION

Abstract interface for a sequence database

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 _

Methods inherieted from Bio::DB::RandomAccessI

get_Seq_by_id

  Title   : get_Seq_by_id
  Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
  Function: Gets a Bio::Seq object by its name
  Returns : a Bio::Seq object
  Args    : the id (as a string) of a sequence
  Throws  : "id does not exist" exception
 
 

get_Seq_by_acc

  Title   : get_Seq_by_acc
  Usage   : $seq = $db->get_Seq_by_acc('X77802');
  Function: Gets a Bio::Seq object by accession number
  Returns : A Bio::Seq object
  Args    : accession number (as a string)
  Throws  : "acc does not exist" exception
 
 

Methods [that were] specific for Bio::DB::SeqI

get_PrimarySeq_stream

  Title   : get_PrimarySeq_stream
  Usage   : $stream = get_PrimarySeq_stream
  Function: Makes a Bio::SeqIO compliant object
            which provides a single method, next_seq
  Returns : Bio::SeqIO
  Args    : none
 
 

get_all_primary_ids

  Title   : get_all_ids
  Usage   : @ids = $seqdb->get_all_primary_ids()
  Function: gives an array of all the primary_ids of the 
            sequence objects in the database. These
            maybe ids (display style) or accession numbers
            or something else completely different - they
            *are not* meaningful outside of this database
            implementation.
  Example :
  Returns : an array of strings
  Args    : none
 
 

get_Seq_by_primary_id

  Title   : get_Seq_by_primary_id
  Usage   : $seq = $db->get_Seq_by_primary_id($primary_id_string);
  Function: Gets a Bio::Seq object by the primary id. The primary
            id in these cases has to come from $db->get_all_primary_ids.
            There is no other way to get (or guess) the primary_ids
            in a database.
 
            The other possibility is to get Bio::PrimarySeqI objects
            via the get_PrimarySeq_stream and the primary_id field
            on these objects are specified as the ids to use here.
  Returns : A Bio::Seq object
  Args    : accession number (as a string)
  Throws  : "acc does not exist" exception