—————————# BioPerl module for FAST::Bio::SeqIO::tinyseqHandler
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Donald Jackson, donald.jackson@bms.com
#
# Copyright Bristol-Myers Squibb
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
FAST::Bio::SeqIO::tinyseq::tinyseqHandler - XML event handlers to support NCBI TinySeq XML parsing
=head1 SYNOPSIS
Do not use this module directly; use the SeqIO handler system:
$stream = FAST::Bio::SeqIO->new( -file => $filename, -format => 'tinyseq' );
while ( my $seq = $stream->next_seq ) {
....
}
=head1 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 L<http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.mod.dtd> for the DTD.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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:
=head1 SEE ALSO
L<FAST::Bio::SeqIO>, L<FAST::Bio::Seq>.
=head1 AUTHOR
Donald Jackson, E<lt>donald.jackson@bms.comE<gt>
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
use
strict;
use
warnings;
# %ATTMAP defines correspondence between TSeq elements, PrimarySeq attributes
# Format: element_name => { xml_attname => pseq_attname }
%ATTMAP
= (
TSeq_sequence
=> {
Data
=>
'-seq'
},
TSeq_gi
=> {
Data
=>
'-primary_id'
},
TSeq_defline
=> {
Data
=>
'-desc'
},
TSeq_sid
=> {
Data
=>
'-sid'
},
TSeq_accver
=> {
Data
=>
'-accver'
},
TSeq_taxid
=> {
Data
=>
'-taxid'
},
TSeq_orgname
=> {
Data
=>
'-organism'
}
);
=head2 new
Title : new
Usage : $handler = FAST::Bio::SeqIO::tinyseq::tinyseqHandler->new()
Function : instantiates a tinyseqHandler for use by
XML::Parser::PerlSAX
Returns : FAST::Bio::SeqIO::tinyseq::tinyseqHandler object
Args : NONE
=cut
sub
new {
my
(
$proto
,
@args
) =
@_
;
my
$class
=
ref
(
$proto
) ||
$proto
;
my
$self
=
bless
({},
$class
);
return
$self
;
}
#######################################
# Event hadling methods for PerlSax #
#######################################
sub
doctype_decl {
my
(
$self
,
$doctype
) =
@_
;
# make sure we have a tinyseq
$self
->throw(
"This document doesn't use the NCBI TinySeq dtd; it's a "
,
$doctype
->{
'SystemId'
} );
}
}
=head2 start_document
Title : start_document
Usage : NONE
Function : start_document handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
=cut
sub
start_document {
my
(
$self
) =
@_
;
$self
->{
'_seqatts'
} = [];
$self
->{
'_elements'
} = [];
}
=head2 end_document
Title : end_document
Usage : NONE
Function : end_document handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
=cut
sub
end_document {
my
(
$self
) =
@_
;
return
$self
->{
'_seqatts'
};
}
=head2 start_element
Title : start_element
Usage : NONE
Function : start_element handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
=cut
sub
start_element {
my
(
$self
,
$starting
) =
@_
;
push
(@{
$self
->{
'_elements'
}},
$starting
);
}
=head2 end_element
Title : end_element
Usage : NONE
Function : end_element handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
=cut
sub
end_element {
my
(
$self
,
$ending
) =
@_
;
# do I have a handler for this element?
my
$ename
=
$ending
->{
'Name'
};
$self
->
$ename
if
(
$self
->can(
$ename
));
}
=head2 characters
Title : characters
Usage : NONE
Function : characters handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
=cut
sub
characters {
my
(
$self
,
$characters
) =
@_
;
my
$data
=
$characters
->{
'Data'
};
return
unless
(
defined
(
$data
) and
$data
=~ /\S/);
my
$current
=
$self
->_current_element;
$current
->{
'Data'
} =
$data
;
}
###########################################
# Element-specific handlers
# called at END of element name
##########################################
=head2 TSeq
Title : TSeq
Usage : NONE
Function : event handler for END of a TSeq element
Returns : loh of parsed sequence atts for FAST::Bio::SeqIO::tinyseq
Args : NONE
=cut
sub
TSeq {
my
(
$self
) =
@_
;
my
%seqatts
;
# map elements onto PrimarySeq keys
while
(
my
$element
=
pop
@{
$self
->{
'_elements'
} }) {
my
$element_name
=
$element
->{
'Name'
};
last
if
(
$element_name
eq
'TSeq'
);
my
$conversion
=
$ATTMAP
{
$element_name
} or
next
;
while
(
my
(
$element_att
,
$pseq_att
) =
each
%$conversion
) {
$seqatts
{
$pseq_att
} =
$element
->{
$element_att
};
}
}
push
(@{
$self
->{
'_seqatts'
} }, \
%seqatts
);
}
#############################################
# Utility method to return current element info
##############################################
=head2 _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
=cut
sub
_current_element {
my
(
$self
) =
@_
;
return
$self
->{
'_elements'
}->[-1];
}
1;