Bio::SeqIO::tinyseq::tUsereContributed PBio::SeqIO::tinyseq::tinyseqHandler(3)NAMEBio::SeqIO::tinyseq::tinyseqHandler - XML event handlers to support
NCBI TinySeq XML parsing
SYNOPSIS
Do not use this module directly; use the SeqIO handler system:
$stream = Bio::SeqIO->new( -file => $filename, -format => 'tinyseq' );
while ( my $seq = $stream->next_seq ) {
....
}
DESCRIPTION
This object provides event handler methods for parsing sequence files
in the NCBI TinySeq XML format. A TinySeq is a lightweight XML file of
sequence information on one or more sequences, analgous to FASTA
format.
See <http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.mod.dtd> for the DTD.
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 the
Bioperl mailing list. 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 of
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
SEE ALSO
Bio::SeqIO, Bio::Seq.
AUTHOR
Donald Jackson, <donald.jackson@bms.com>
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : $handler = Bio::SeqIO::tinyseq::tinyseqHandler->new()
Function : instantiates a tinyseqHandler for use by
XML::Parser::PerlSAX
Returns : Bio::SeqIO::tinyseq::tinyseqHandler object
Args : NONE
start_document
Title : start_document
Usage : NONE
Function : start_document handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
end_document
Title : end_document
Usage : NONE
Function : end_document handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
start_element
Title : start_element
Usage : NONE
Function : start_element handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
end_element
Title : end_element
Usage : NONE
Function : end_element handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
characters
Title : characters
Usage : NONE
Function : characters handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
TSeq
Title : TSeq
Usage : NONE
Function : event handler for END of a TSeq element
Returns : loh of parsed sequence atts for Bio::SeqIO::tinyseq
Args : NONE
_current_element
Title : _current_element
Usage : Internal method
Function : Utility method to return current element info
Returns : XML::Parser::PerlSAX hash for current element
Args : NONE
perl v5.14.12011-0Bio::SeqIO::tinyseq::tinyseqHandler(3)
