# some of the following code was pillaged from the CPAN module
# XML::Handler::Subs
#
# Copyright (C) 1999 Ken MacLeod
# XML::Handler::XMLWriter is free software; you can redistribute it and/or
# modify it under the same terms as Perl itself.
#
# BioPerl module for Bio::SeqIO::game::gameSubs
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sheldon McKay <mckays@cshl.edu>
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::game::gameSubs -- a base class for game-XML parsing
=head1 SYNOPSIS
Not used directly
=head1 DESCRIPTION
A bag of tricks for game-XML parsing. The PerlSAX handler methods were
stolen from Chris Mungall's XML base class, which he stole from Ken MacLeod's
XML::Handler::Subs
=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 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
=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:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Sheldon McKay
Email mckays@cshl.edu
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::SeqIO::game::gameSubs;
use XML::Parser::PerlSAX;
use UNIVERSAL;
use strict;
use vars qw {};
use base qw(Bio::Root::Root);
=head2 new
Title : new
Usage : not used directly
Returns : a gameHandler object
Args : an XML filename
=cut
sub new {
my $type = shift;
my $file = shift || "";
my $self = (@_ == 1) ? { %{ (shift) } } : { @_ };
if ($file) {
$self->{file} = $file;
}
return bless $self, $type;
}
=head2 go
Title : go
Usage : not used directly
Function: starts PerlSAX XML parsing
=cut
sub go {
my $self = shift;
XML::Parser::PerlSAX->new->parse(Source => { SystemId => "$self->{file}" },
Handler => $self);
}
=head2 start_document
Title : start_document
Usage : not used directly
=cut
sub start_document {
my ($self, $document) = @_;
$self->{Names} = [];
$self->{Nodes} = [];
}
=head2 end_document
Title : end_document
Usage : not used directly
=cut
sub end_document {
my ($self, $document) = @_;
delete $self->{Names};
delete $self->{Nodes};
return();
}
=head2 start_element
Title : start_element
Usage : not used directly
=cut
sub start_element {
my ($self, $element) = @_;
$element->{Children} = [];
$element->{Name} =~ tr/A-Z/a-z/;
push @{$self->{Names}}, $element->{Name};
push @{$self->{Nodes}}, $element;
my $el_name = "s_" . $element->{Name};
$el_name =~ s/[^a-zA-Z0-9_]/_/g;
if ($ENV{DEBUG_XML_SUBS}) {
print STDERR "xml_subs:$el_name\n";
}
if ($self->can($el_name)) {
$self->$el_name($element);
return 1;
}
return 0;
}
=head2 end_element
Title : end_element
Usage : not used directly
=cut
sub end_element {
my ($self, $element) = @_;
my $called_sub = 0;
$element->{Name} =~ tr/A-Z/a-z/;
my $el_name = "e_" . $element->{Name};
$el_name =~ s/[^a-zA-Z0-9_]/_/g;
my $rval = 0;
if ($ENV{DEBUG_XML_SUBS}) {
print STDERR "xml_subs:$el_name\n";
}
if ($self->can($ {el_name})) {
$rval = $self->$el_name($element) || 0;
$called_sub = 1;
}
my $curr_element = $self->{Nodes}->[$#{$self->{Nodes}}];
pop @{$self->{Names}};
pop @{$self->{Nodes}};
if ($rval eq -1 || !$called_sub) {
if (@{$self->{Nodes}}) {
my $parent = $self->{Nodes}->[$#{$self->{Nodes}}];
push(@{$parent->{Children}}, $curr_element);
$parent->{"_".$curr_element->{Name}} = $curr_element;
}
}
return $called_sub;
}
=head2 characters
Title : characters
Usage : not used directly
=cut
sub characters {
my ($self, $characters) = @_;
my $str = $self->strip_characters($characters->{Data});
my $curr_element = $self->curr_element();
$curr_element->{Characters} .= $str;
0;
}
=head2 strip_characters
Title : strip_characters
Usage : not used directly
Function: cleans up XML element contents
=cut
sub strip_characters {
my ($self, $str) = @_;
$str =~ s/^[ \n\t]* *//g;
$str =~ s/ *[\n\t]*$//g;
$str;
}
=head2 curr_element
Title : curr_element
Usage : not used directly
Function: returns the currently open element
=cut
sub curr_element {
my $self = shift;
return $self->{Nodes}->[-1];
}
=head2 flush
Title : flush
Usage : $self->flush($element) # or $element->flush
Function: prune a branch from the XML tree
Returns : true if successful
Args : an element object (optional)
=cut
sub flush {
my $self = shift;
my $victim = shift || $self->curr_element;
$victim = {};
return 1;
}
# throw a non-fatal warning
=head2 complain
Title : complain
Usage : $self->complain("This is terrible; I am not happy")
Function: throw a non-fatal warning, formats message for pretty-printing
Returns : nothing
Args : a list of strings
=cut
sub complain {
my $self = shift;
return 0 unless $self->{verbose};
my $msg = join '', @_;
$msg =~ s/\n/ /g;
my @msg = split /\s+/, $msg;
my $new_msg = '';
for ( @msg ) {
my ($last_chunk) = $new_msg =~ /\n?(.+)$/;
my $l = $last_chunk ? length $last_chunk : 0;
if ( (length $_) + $l > 45 ) {
$new_msg .= "\n$_ ";
}
else {
$new_msg .= $_ . ' ';
}
}
$self->warn($new_msg);
}
=head2 dbxref
Title : dbxref
Usage : $self->db_xref($el, $tags)
Function: an internal method to flatten dbxref elements
Returns : the db_xref (eg wormbase:C02D5.1)
Args : an element object (reqd) and a hash ref of tag/values (optional)
=cut
sub dbxref {
my ($self, $el, $tags) = @_;
$tags ||= $self->{curr_tags};
my $db = $el->{_xref_db}->{Characters};
my $acc = $el->{_unique_id} ||
$el->{_db_xref_id} ||
$el->{_xref_db_id};
my $id = $acc->{Characters} or return 0;
$self->flush( $el );
# capture both the database and accession number
$id= $id =~ /^\w+$/ ? "$db:$id" : $id;
$tags->{dbxref} ||= [];
push @{$tags->{dbxref}}, $id;
$id;
}
=head2 comment
Title : comment
Usage : $self->comment($comment_element)
Function: a method to flatten comment elements
Returns : a string
Args : an comment element (reqd) and a hash ref of tag/values (optional)
Note : The hope here is that we can unflatten structured comments
in game-derived annotations happen to make a return trip
=cut
sub comment {
my ($self, $el, $tags) = @_;
$tags ||= $self->{curr_tags};
my $text = $el->{_text}->{Characters};
my $pers = $el->{_person}->{Characters};
my $date = $el->{_date}->{Characters};
my $int = $el->{_internal}->{Characters};
$self->flush( $el );
my $comment = "person=$pers; " if $pers;
$comment .= "date=$date; " if $date;
$comment .= "internal=$int; " if $int;
$comment .= "text=$text" if $text;
$tags->{comment} ||= [];
push @{$tags->{comment}}, $comment;
$comment;
}
=head2 property
Title : property
Usage : $self->property($property_element)
Function: an internal method to flatten property elements
Returns : a hash reference
Args : an property/output element (reqd) and a hash ref of tag/values (optional)
Note: This method is aliased to 'output' to handle structurally identical output elements
=cut
*output = \&property;
sub property {
my ($self, $el, $tags) = @_;
$tags ||= $self->{curr_tags};
my $key = $el->{_type}->{Characters};
my $value = $el->{_value}->{Characters};
$self->flush( $el );
$tags->{$key} ||= [];
push @{$tags->{$key}}, $value;
$tags;
}
=head2 evidence
Title : evidence
Usage : $self->evidence($evidence_element)
Function: a method to flatten evidence elements
Returns : a string
Args : an evidence element
=cut
sub evidence {
my ($self, $el) = @_;
my $tags = $self->{curr_tags};
my $text = $el->{Characters} or return 0;
my $type = $el->{Attributes}->{type};
my $res = $el->{Attributes}->{result};
$self->flush( $el );
my $evidence = "type=$type; " if $type;
$evidence .= "result=$res; " if $res;
$evidence .= "evidence=$text";
$tags->{evidence}||= [];
push @{$tags->{evidence}}, $evidence;
$evidence;
}
=head2 date
Title : date
Usage : $self->date($date_element)
Function: a method to flatten date elements
Returns : true if successful
Args : a date element
=cut
sub date {
my ($self, $el) = @_;
my $tags = $self->{curr_tags};
my $date = $el->{Characters} or return 0;
my $stamp = $el->{Attributes}->{timestamp};
$self->flush( $el );
$tags->{date} ||= [];
push @{$tags->{date}}, $date;
$tags->{timestamp} ||= [];
push @{$tags->{timestamp}}, $stamp;
1;
}
=head2 protein_id
Title : protein_id
Usage : $pid = $self->protein_id($cds, $standard_name)
Function: a method to search for a protein name
Returns : a string
Args : the CDS object plus the transcript\'s 'standard_name'
=cut
sub protein_id {
my ($self, $cds, $sn) = @_;
my $psn;
if ( $cds->has_tag('protein_id') ) {
($psn) = $cds->get_tag_values('protein_id');
}
elsif ( $cds->has_tag('product') ) {
($psn) = $cds->get_tag_values('product');
$psn =~ s/.+?(\S+)$/$1/;
}
elsif ( $cds->has_tag('gene') ) {
($psn) = $cds->get_tag_values('gene');
}
elsif ( $sn ) {
$psn = $sn;
}
else {
$self->complain("Could not find an ID for the protein");
return '';
}
$psn =~ s/-R/-P/;
return $psn;
}
1;