Bio::SeqIO tigrxml
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Summary
Bio::SeqIO::tigrxml - Parse TIGR (new) XML
Package variables
No package variables defined.
Included modules
Bio::Annotation::Comment
Bio::Annotation::DBLink
Bio::Annotation::Reference
Bio::Seq::SeqFactory
Bio::SeqFeature::Generic
Bio::Species
Data::Dumper
List::Util qw ( min max )
XML::SAX
XML::SAX::Writer
Inherit
Bio::SeqIO XML::SAX::Base
Synopsis
  use Bio::SeqIO;
my $in = Bio::SeqIO->new(-format => 'tigrcoordset',
-file => 'file.xml');
while( my $seq = $in->next_seq ) { # do something... }
Description
This is a parser for TIGR Coordset XML for their in-progress
annotation dbs.
Methods
_initialize
No description
Code
next_seq
No description
Code
start_document
No description
Code
end_document
No description
Code
start_element
No description
Code
end_element
No description
Code
characters
No description
Code
assert
No description
Code
Methods description
None available.
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my ($self) = shift;
    $self->SUPER::_initialize(@_);
    $self->{'_parser'} = XML::SAX::ParserFactory->parser('Handler' => $self);
    if( ! defined $self->sequence_factory ) {
	$self->sequence_factory(Bio::Seq::SeqFactory->new
				(-verbose => $self->verbose(), 
				 -type => 'Bio::Seq::RichSeq'));
    }
    return;
}
next_seqdescriptionprevnextTop
sub next_seq {
        my $self = shift;
    if( @{$self->{'_seendata'}->{'_seqs'} || []} || 
	eof($self->_fh)) { 
	return shift @{$self->{'_seendata'}->{'_seqs'}};
    }
    $self->{'_parser'}->parse_file($self->_fh);
    return shift @{$self->{'_seendata'}->{'_seqs'}};
}

# XML::SAX::Base methods
}
start_documentdescriptionprevnextTop
sub start_document {
    my ($self,$doc) = @_;
    $self->{'_seendata'} = {'_seqs'    => [],
			    '_authors' => [],
			    '_feats'   => [] };
    $self->SUPER::start_document($doc);
}
end_documentdescriptionprevnextTop
sub end_document {
     my ($self,$doc) = @_;
    $self->SUPER::end_document($doc);
}
start_elementdescriptionprevnextTop
sub start_element {
    my ($self,$ele) = @_;
    # attributes
my $name = uc $ele->{'LocalName'}; my $attr = $ele->{'Attributes'}; my $seqid = defined $self->{'_seendata'}->{'_seqs'}->[-1] ? $self->{'_seendata'}->{'_seqs'}->[-1]->display_id : undef; # we're going to try and be SO-nice here
if( $name eq 'ASSEMBLY' ) { # New sequence
my ($len) = $attr->{'{}COORDS'}->{'Value'} =~ /\d+\-(\d+)/; push @{$self->{'_seendata'}->{'_seqs'}}, $self->sequence_factory->create ( -display_id => $attr->{'{}ASMBL_ID'}->{'Value'}, -length => $len, ); } elsif( $name eq 'HEADER' ) { } elsif( $name eq 'CLONE_NAME' ) { } elsif( $name eq 'ORGANISM' ) { } elsif( $name eq 'AUTHOR_LIST' ) { $self->{'_seendata'}->{'_authors'} = []; } elsif( $name eq 'TU' ) { # gene feature
my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $fname = $attr->{'{}FEAT_NAME'}->{'Value'}; my $f = Bio::SeqFeature::Generic->new (-seq_id => $seqid, -start => $s, -end => $e, -strand => $strand, -primary_tag => 'gene', # what does this really map to?
-source_tag => $Default_Source, -tag => { 'Note' => $attr->{'{}COM_NAME'}->{'Value'}, 'ID' => $fname, 'locus' => $attr->{'{}LOCUS'}->{'Value'}, 'pub_locus' => $attr->{'{}PUB_LOCUS'}->{'Value'}, 'alt_locus' => $attr->{'{}ALT_LOCUS'}->{'Value'}, 'pub_comment' => $attr->{'{}PUB_COMMENT'}->{'Value'}, } ); push @{$self->{'_seendata'}->{'_feats'}}, $f; # add this feature to the current sequence
$self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'MODEL' ) { # mRNA/transcript
# reset the UTRs
$self->{'_seendata'}->{"five_prime_UTR"}= undef; $self->{'_seendata'}->{"three_prime_UTR"} = undef; my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $parent = $self->{'_seendata'}->{'_feats'}->[-1]; my ($parentid) = $parent->get_tag_values('ID'); my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'transcript', -source_tag => $Default_Source, -start => $s, # we use parent start/stop because 'MODEL' means CDS start/stop
-end => $e, # but we want to reflect
-strand => $strand, -seq_id => $seqid, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, 'Parent' => $parentid, 'Note' => $attr->{'{}COMMENT'}->{'Value'}, }); $parent->add_SeqFeature($f); push @{$self->{'_seendata'}->{'_feats'}}, $f; $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'EXON' ) { # exon feature
my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $parent = $self->{'_seendata'}->{'_feats'}->[-1]; my ($parentid) = $parent->get_tag_values('ID'); my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'exon', -source_tag => $Default_Source, -seq_id => $seqid, -start => $s, -end => $e, -strand => $strand, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, 'Parent' => $parentid, }); $parent->add_SeqFeature($f,'EXPAND'); $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); # we'll still just add exons to the transcript
} elsif( $name eq 'PROTEIN_SEQ' ) { } elsif( $name eq 'CDS' ) { # CDS will be the translation of the transcript
my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $parent = $self->{'_seendata'}->{'_feats'}->[-1]; my ($parentid) = $parent->get_tag_values('ID'); $self->assert($parent->primary_tag eq 'transcript', 'Testing for primary tag equivalent to mRNA'); $self->assert($parent->strand == $strand || abs($s-$e) == 0, 'Testing that parent feature and current feature strand are equal '. $parentid. ' '.$attr->{'{}FEAT_NAME'}->{'Value'}); my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'CDS', -source_tag => $Default_Source, -seq_id => $seqid, -start => $s, -end => $e, -strand => $parent->strand, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, 'Parent' => $parentid, # should be the mRNA
}); $parent->add_SeqFeature($f); $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'RNA-EXON' ) { my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $parent = $self->{'_seendata'}->{'_feats'}->[-1]; my ($parentid) = $parent->get_tag_values('ID'); my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'tRNA_exon', # tRNA_exon?
-source_tag => $Default_Source, -seq_id => $seqid, -start => $s, -end => $e, -strand => $strand, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, 'Parent' => $parentid, } ); $parent->add_SeqFeature($f); $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'PRE-TRNA' ) { # tRNA gene
my ($s,$e) = ( $attr->{'{}COORDS'}->{'Value'} =~/(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $f = Bio::SeqFeature::Generic->new ( -primary_tag => 'tRNA_coding_gene', -source_tag => $Default_Source, -seq_id => $seqid, -start => $s, -end => $e, -strand => $strand, -tag => {'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, } ); push @{$self->{'_seendata'}->{'_feats'}}, $f; $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'TRNA' ) { # tRNA transcript
my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $parent = $self->{'_seendata'}->{'_feats'}->[-1]; my ($parentid) = $parent->get_tag_values('ID'); my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'tRNA_primary_transcript', -source_tag => $Default_Source, -start => $s, -end => $e, -strand => $strand, -seq_id => $seqid, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, 'Parent' => $parentid, 'Note' => $attr->{'{}COM_NAME'}->{'Value'}, 'anticodon' => $attr->{'{}ANTICODON'}->{'Value'}, 'pub_locus' => $attr->{'{}PUB_LOCUS'}->{'Value'}, }); $parent->add_SeqFeature($f); push @{$self->{'_seendata'}->{'_feats'}}, $f; $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'REPEAT_LIST' ) { } elsif( $name eq 'REPEAT' ) { my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'simple_repeat', -source_tag => $Default_Source, -seq_id => $seqid, -start => $s, -end => $e, -stand => $strand, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, }); push @{$self->{'_seendata'}->{'_feats'}}, $f; $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif ( $name eq 'AUTHOR' ) { } elsif( $name eq 'GB_DESCRIPTION' ) { } elsif( $name eq 'GB_COMMENT' ) { } elsif( $name eq 'LINEAGE' ) { } else { $self->warn("Unknown element $name, ignored\n"); } push @{$self->{'_state'}}, $name; $self->SUPER::start_element($ele);
}
end_elementdescriptionprevnextTop
sub end_element {
    my ($self,$ele) = @_;
    pop @{$self->{'_state'}};
    my $name = $ele->{'LocalName'};
    my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1];
    if( $name eq 'AUTHOR_LIST' ) {
	if( $curseq->can('annotation') ) {
	    $curseq->annotation->add_Annotation
		('reference',Bio::Annotation::Reference->new
		 (-authors => join(',',@{$self->{'_seendata'}->{'_authors'}}))
		 );	    
	}
	$self->{'_seendata'}->{'_authors'} = [];
    } elsif( $name eq 'ASSEMBLY' ) {
	if( @{$self->{'_seendata'}->{'_feats'} || []} ) {
	    $self->warn("Leftover features which were not finished!");
	}
	$self->debug("end element for ASSEMBLY ". $curseq->display_id. "\n");
    } elsif( $name eq 'TU' || 
	     $name eq 'TRNA'  || $name eq 'PRE-TRNA' || 
	     $name eq 'REPEAT' ) {
	pop @{$self->{'_seendata'}->{'_feats'}};
    } elsif( $name eq 'MODEL' ) {
	# This is all to for adding UTRs	
my $model = pop @{$self->{'_seendata'}->{'_feats'}}; my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1]; # sort smallest to largest, don't forget about
# strandedness
my ($parentid) = $model->get_tag_values('Parent'); my @features = $model->get_SeqFeatures(); my @exons = sort { $a->start <=> $b->start } grep { $_->primary_tag eq 'exon' } @features; my @cdsexons = sort { $a->start <=> $b->start } grep { $_->primary_tag eq 'CDS' } @features; # look at the exons, find those which come after the model start
my $cdsexon = shift @cdsexons; my $exon = shift @exons; # first exon
if( ! defined $cdsexon ) { $self->warn( "no CDS exons $parentid!"); return; } elsif( ! defined $exon ) { $self->warn("no exons $parentid!" ); return; } my $utrct = 1; while( defined $exon && $exon->start < $cdsexon->start ) { my ($pid) = $exon->get_tag_values('Parent'); $self->debug("LeftPhase: tu-id $parentid mrna-id $pid exon is ". $exon->location->to_FTstring. " CDSexon is ".$cdsexon->location->to_FTstring."\n"); my $utr = Bio::SeqFeature::Generic->new (-seq_id => $exon->seq_id, -strand => $exon->strand, -primary_tag => $exon->strand > 0 ? "five_prime_UTR" : "three_prime_UTR", -source_tag => $Default_Source, -tag => { 'ID' => "$pid.UTR".$utrct++, 'Parent' => $pid }, ); my ($ns,$ne); if( $utr->primary_tag eq 'five_prime_UTR' ) { $ns = $exon->start; $ne = min ( $exon->end, $cdsexon->start - 1); } else { $ne = min( $exon->end, $cdsexon->start - 1); $ns = $exon->start; } $utr->start($ns); $utr->end($ne); $model->add_SeqFeature($utr); $curseq->add_SeqFeature($utr); $exon = shift @exons; } @exons = sort { $a->start <=> $b->start } grep {$_->primary_tag eq 'exon' } @features; @cdsexons = sort { $a->start <=> $b->start } grep { $_->primary_tag eq 'CDS' } @features; $cdsexon = pop @cdsexons; $exon = pop @exons; if( ! defined $cdsexon ) { $self->warn( "no CDS exons $parentid!"); return; } elsif( ! defined $exon ) { $self->warn("no exons $parentid!" ); return; } $utrct = 1; while( defined $exon &&$exon->end > $cdsexon->end ) { my ($pid) = $exon->get_tag_values('Parent'); $self->debug("RightPhase: tu-id $parentid mrna-id $pid exon is ". $exon->location->to_FTstring. " CDSexon is ".$cdsexon->location->to_FTstring."\n"); my $utr = Bio::SeqFeature::Generic->new (-seq_id => $exon->seq_id, -strand => $exon->strand, -primary_tag => $exon->strand < 0 ? "five_prime_UTR" : "three_prime_UTR", -source_tag => $Default_Source, -tag => { 'Parent' => $pid, 'ID' => "$pid.UTR".$utrct++, } ); my ($ns,$ne); if( $utr->primary_tag eq 'three_prime_UTR' ) { $ns = max ( $exon->start, $cdsexon->end + 1); $ne = $exon->end; } else { $ns = $cdsexon->end+1; $ne = max ( $exon->end, $cdsexon->start + 1); } $utr->start($ns); $utr->end($ne); $model->add_SeqFeature($utr); $curseq->add_SeqFeature($utr); $exon = pop @exons; } } $self->SUPER::end_element($ele);
}
charactersdescriptionprevnextTop
sub characters {
    my ($self,$data) = @_;
    if( ! @{$self->{'_state'}} ) {
	$self->warn("Calling characters with no previous start_element call. Ignoring data");
    } else {
	my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1];
	my $curfeat = $self->{'_seendata'}->{'_feats'}->[-1];
	my $name = $self->{'_state'}->[-1];	
	if( defined $curseq ) { 
	    if( $name eq 'CLONE_NAME' ) {
		$self->debug("Clone name is ",$data->{'Data'}, "\n");
		$curseq->display_id($data->{'Data'});
	    } elsif( $name eq 'ORGANISM' ) {
		my ($genus,$species,$subspec) = split(/\s+/,$data->{Data},3);
		$curseq->species(Bio::Species->new(
						   -classification => 
						   [$species,$genus],
						   -sub_species => $species));
	    } elsif( $name eq 'LINEAGE' ) {
		$curseq->species->classification( 
				  [ 
				    $curseq->species->species,
				    $curseq->species->genus, 
				    reverse  (map { s/^\s+//; 
						    s/\s+$//; $_; } 
					      split /[;\.]+/,$data->{'Data'} ),
				    ]
				  );
	    } elsif( $name eq 'AUTHOR' ) {
		push @{$self->{'_seendata'}->{'_authors'}}, $data->{'Data'};
	    }
	}
	if( defined $curfeat ) {
	    if( $name eq 'EXON' ) { # exon feature
} elsif( $name eq 'RNA-EXON' ) { } elsif( $name eq 'PROTEIN_SEQ' ) { $curfeat->add_tag_value('translation',$data->{'Data'}); } elsif( $name eq 'CDS' ) { } elsif( $name eq 'PRE-TRNA' ) { # tRNA gene
} elsif( $name eq 'TRNA' ) { # tRNA transcript
} elsif( $name eq 'REPEAT_LIST' ) { } elsif( $name eq 'REPEAT' ) { $curfeat->add_tag_value('Note',$data->{'Data'}); } elsif( $name eq 'GB_COMMENT' ) { $curseq->annotation->add_Annotation ('comment', Bio::Annotation::Comment->new(-text => $data->{'Data'})); } elsif( $name eq 'GB_DESCRIPTION' ) { $curseq->description($data->{'Data'}); } } } $self->SUPER::characters($data);
}
assertdescriptionprevnextTop
sub assert {
     my ($self,$test,$msg) = @_;
    $self->throw($msg) unless $test;
}
1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _