| Bio::ClusterIO::dbsnp(3pm) | User Contributed Perl Documentation | Bio::ClusterIO::dbsnp(3pm) |
Bio::ClusterIO::dbsnp - dbSNP input stream
Do not use this module directly. Use it via the Bio::ClusterIO class.
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/).
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.
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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.
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:
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Allen Day <allenday@ucla.edu>
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
Title : end_document Usage : $parser->end_document; Function: SAX method to indicate finishing parsing a new document Returns : none Args : none
Title : start_element Usage : $parser->start_element($data) Function: SAX method to indicate starting a new element Returns : none Args : hash ref for data
Title : end_element Usage : $parser->end_element($data) Function: Signals finishing an element Returns : none Args : hash ref for data
Title : characters Usage : $parser->characters($data) Function: Signals new characters to be processed Returns : characters read Args : hash ref with the key 'Data'
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)
| 2022-03-27 | perl v5.34.0 |