Bio::ClusterIO::dbsnp.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::ClusterIO::dbsnp - dbSNP input stream

SYNOPSIS

Do not use this module directly. Use it via the Bio::ClusterIO class.

DESCRIPTION

Parse dbSNP XML files, one refSNP entry at a time. Note this handles dbSNPp output generated by NBCI's eutils and does NOT parse output derived from SNP's XML format (found at ftp://ftp.ncbi.nih.gov/snp/).

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

Allen Day <allenday@ucla.edu>

APPENDIX

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

next_cluster

  Title   : next_cluster
  Usage   : $dbsnp = $stream->next_cluster()
  Function: returns the next refSNP in the stream
  Returns : Bio::Variation::SNP object representing composite refSNP
            and its component subSNP(s).
  Args    : NONE
 
 

SAX methods

start_document

  Title   : start_document
  Usage   : $parser->start_document;
  Function: SAX method to indicate starting to parse a new document.
            Creates a Bio::Variation::SNP
  Returns : none
  Args    : none
 
 

end_document

  Title   : end_document
  Usage   : $parser->end_document;
  Function: SAX method to indicate finishing parsing a new document
  Returns : none
  Args    : none
 
 

start_element

  Title   : start_element
  Usage   : $parser->start_element($data)
  Function: SAX method to indicate starting a new element
  Returns : none
  Args    : hash ref for data
 
 

end_element

  Title   : end_element
  Usage   : $parser->end_element($data)
  Function: Signals finishing an element
  Returns : none
  Args    : hash ref for data
 
 

characters

  Title   : characters
  Usage   : $parser->characters($data)
  Function: Signals new characters to be processed
  Returns : characters read
  Args    : hash ref with the key 'Data'
 
 

use_tempfile

  Title   : use_tempfile
  Usage   : $obj->use_tempfile($newval)
  Function: Get/Set boolean flag on whether or not use a tempfile
  Example : 
  Returns : value of use_tempfile
  Args    : newvalue (optional)