Bio::SeqIO tigr
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Summary
Bio::SeqIO::tigr - TIGR XML sequence input/output stream
Package variables
No package variables defined.
Included modules
Bio::Annotation::Comment
Bio::Seq::RichSeq(1)
Bio::Seq::RichSeq(2)
Bio::Seq::SeqFactory
Bio::SeqFeature::Generic
Bio::Species
Data::Dumper
Error qw /:try/
Inherit
Bio::SeqIO
Synopsis
Do not use this module directly. Use it via the Bio::SeqIO class.
Description
This object can transform Bio::Seq objects to and from efa flat
file databases.
Methods
_initialize
No description
Code
next_seq()
No description
Code
_process
No description
Code
_process_tigr
No description
Code
_process_pseudochromosome
No description
Code
_process_assembly
No description
Code
_process_assembly_seq()
No description
Code
_process_coordset($)
No description
Code
_process_header
No description
Code
_process_gene_list
No description
Code
_process_protein_coding
No description
Code
_process_rna_genes
No description
Code
_process_misc_info
No description
Code
_process_repeat_list
No description
Code
_process_tiling_path
No description
Code
_process_scaffold
No description
Code
_process_tu
No description
Code
_process_gene_info
No description
Code
_build_location
No description
Code
_process_model
No description
Code
_process_cdna_support
No description
Code
_process_exon
No description
Code
_process_cds
No description
Code
_process_utrs
No description
Code
_process_left_utr
No description
Code
_process_right_utr
No description
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_process_ext_utr
No description
Code
_readtag
No description
Code
_readline
No description
Code
throw
No description
Code
Methods description
None available.
Methods code
_initializedescriptionprevnextTop
sub _initialize {
	my($self, @args) = @_;

	$self->SUPER::_initialize(@args);
	$self->sequence_factory(Bio::Seq::SeqFactory->new(
			-type => 'Bio::Seq::RichSeq')
	);

	# Parse the document
$self->_process();
}
next_seq()descriptionprevnextTop
sub next_seq() {
	my ($self) = @_;
	
	# Check for any more sequences
return if !defined($self->{_sequences}) or scalar(@{$self->{_sequences}}) < 1; # get the next sequence
my $seq = shift(@{ $self->{_sequences} } ); # Get the 5' and 3' ends
my ($source) = grep { $_->primary_tag() eq 'source' } $seq->get_SeqFeatures(); my ($end5) = $source->get_tag_values('end5'); my ($end3) = $source->get_tag_values('end3'); # Sort the 5' and 3':
my ($start, $end) = ( $end5 < $end3 ? ( $end5, $end3 ) : ( $end3, $end5 ) ); # make the start a perl index
$start -= 1; # Figure out the length
my $length = $end - $start; # check to make sure $start >= 0 and $end <= length(assembly_seq)
if($start < 0) { throw Bio::Root::OutOfRange("the sequence start is $start < 0"); } elsif($end > length($self->{_assembly}->{seq})) { throw Bio::Root::OutOfRange("the sequence end is $end < " . length($self->{_assembly}->{seq})); } elsif($start >= $end) { throw Bio::Root::OutOfRange("the sequence start is after end $start >= $end"); } # Get and set the real sequence
$seq->seq(substr($self->{_assembly}->{seq}, $start, $length)); if( $end5 > $end3 ) { # Reverse complement the sequence
$seq->seq( $seq->primary_seq()->revcom()->seq() ); } # add the translation to each CDS
foreach my $feat ($seq->get_SeqFeatures()) { next if $feat->primary_tag() ne "CDS"; # Check for an invalid protein
try { # Get the subsq
my $cds = Bio::PrimarySeq->new( -strand => 1, -id => $seq->accession_number(), -seq => $seq->subseq($feat->location()) ); # Translate it
my $trans = $cds->translate(undef, undef, undef, undef, 1, 1)->seq(); # Add the tag
$feat->add_tag_value(translation => $trans); } catch Bio::Root::Exception with { print STDERR 'TIGR strikes again, the CDS is not a valid protein: ', $seq->accession_number(), "\n" if $self->verbose() > 0; }; } # Set the display id to the accession number if there
# is no display id
$seq->display_id( $seq->accession_number() ) unless $seq->display_id(); return $seq;
}
_processdescriptionprevnextTop
sub _process {
	my($self) = @_;
	my $line;
	my $tu = undef;

	$line = $self->_readline();
	do {
		if($line =~ /<\?xml\s+version\s+=\s+"\d+\.\d+"\?>/o) {
			# do nothing
} elsif ($line =~ /<!DOCTYPE (\w+) SYSTEM "[\w\.]+">/o) { $self->throw("DOCTYPE of $1, not TIGR!") if $1 ne "TIGR" ; } elsif ($line =~ /<TIGR>/o) { $self->_pushback($line); $self->_process_tigr(); } elsif ($line =~ /<ASSEMBLY.*?>/o) { $self->_pushback($line); $self->_process_assembly(); } elsif ($line =~ /<\/TIGR>/o) { $self->{'eof'} = 1; return; } else { $self->throw("Unknown or Invalid process directive:", join('', ($line =~ /^\s*(<[^>]+>)/o))); } $line = $self->_readline(); } while( defined( $line ) );
}
_process_tigrdescriptionprevnextTop
sub _process_tigr {
	my($self) = @_;
	my $line;

	$line = $self->_readline();
	if($line !~ /<TIGR>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_tigr called but no ",
		             "<TIGR> found in stream");
	}

	$line = $self->_readline();
	if($line =~ /<PSEUDOCHROMOSOME>/o) {
		$self->_pushback($line);
		$self->_process_pseudochromosome();
	} elsif ($line =~ /<ASSEMBLY.*?>/o) {
		$self->_pushback($line);
		$self->_process_assembly();
	}
}
_process_pseudochromosomedescriptionprevnextTop
sub _process_pseudochromosome {
	my($self) = @_;
	my $line;

	$line = $self->_readline();
	return if $line !~ /<PSEUDOCHROMOSOME>/o;

	$line = $self->_readline();

	if($line =~ /<SCAFFOLD>/o) {
		$self->_pushback($line);
		$self->_process_scaffold();
		$line = $self->_readline();
	} else {
		$self->warn( "No Scaffold found in <PSUEDOCHROMOSOME> this " .
		             "is a violation of the TIGR dtd, but we ignore " .
		             "it so we are ignoring the error\n"
		);
	}

	if($line =~ /<ASSEMBLY.*>/o) {
		$self->_pushback($line);
		$self->_process_assembly();
		$line = $self->_readline();
	} else {
		$self->throw("Missing required ASSEMBLY in <PSEUDOCHROMOSOME>");
	}

	if($line =~ /<\/PSEUDOCHROMOSOME>/) {
		return;
	}

	$self->throw("Reached end of _process_psuedochromosome");
}
_process_assemblydescriptionprevnextTop
sub _process_assembly {
	my($self) = @_;
	my $line;

	$line = $self->_readline();
	if($line !~ /<ASSEMBLY([^>]*)>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_assembly called ",
		             "but no <ASSEMBLY> found in stream");
	}

	my %attribs = ($1 =~ /(\w+)\s*=\s+"(.*?)"/og);
	$self->{_assembly}->{date}       = $attribs{CURRENT_DATE};
	$self->{_assembly}->{db}         = $attribs{DATABASE};
	$self->{_assembly}->{chromosome} = $attribs{CHROMOSOME};

	$line = $self->_readline();
	my($attr, $val); 
	if(($attr, $val) = ($line =~ /<ASMBL_ID([^>]*)>([^<]*)<\/ASMBL_ID>/o)) {
		%attribs = ($attr =~ /(\w+)\s*=\s+"(.*?)"/og);
		$self->{_assembly}->{clone_name} = $attribs{CLONE_NAME};
		$self->{_assembly}->{clone} = $val;
		$line = $self->_readtag();
	} else {
		$self->throw("Required <ASMBL_ID> missing");
	}

	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		my $cs = $self->_process_coordset();

		$self->{_assembly}->{end5} = $cs->{end5};
		$self->{_assembly}->{end3} = $cs->{end3};

		$line = $self->_readline();
	} else {
		$self->throw("Required <COORDSET> missing");
	}

	if($line =~ /<HEADER>/o) {
		$self->_pushback($line);
		$self->_process_header();
		$line = $self->_readline();
	} else {
		$self->throw("Required <HEADER> missing");
	}

	if($line =~ /<TILING_PATH>/o) {
		$self->_pushback($line);
		$self->_process_tiling_path();
		$line = $self->_readline();
	}

	if($line =~ /<GENE_LIST>/o) {
		$self->_pushback($line);
		$self->_process_gene_list();
		$line = $self->_readline();
	} else {
		$self->throw("Required <GENE_LIST> missing");
	}

	if($line =~ /<MISC_INFO>/o) {
		$self->_pushback($line);
		$self->_process_misc_info();
		$line = $self->_readline();
	}

	if($line =~ /<REPEAT_LIST>/o) {
		$self->_pushback($line);
		$self->_process_repeat_list();
		$line = $self->_readline();
	}

	if($line =~ /<ASSEMBLY_SEQUENCE>/o) {
		$self->_pushback($line);
		$self->_process_assembly_seq();
		$line = $self->_readline();
	} else {
		$self->throw("Required <ASSEMBLY_SEQUENCE> missing");
	}

	if($line =~ /<\/ASSEMBLY>/o) {
		return;
	}
	$self->throw("Reached the end of <ASSEMBLY>");
}
_process_assembly_seq()descriptionprevnextTop
sub _process_assembly_seq() {
	my ($self) = @_;
	my $line;
	
	$line = $self->_readline();
	if($line !~ /<ASSEMBLY_SEQUENCE>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_assembly_seq called ".
			     "with no <ASSEMBLY_SEQUENCE> in the stream");
	}

	# Protect agains lots of smaller lines
my @chunks; do { $line = $self->_readline(); last unless $line; my $seq; if (($seq) = ($line =~ /^\s*(\w+)\s*$/o)) { push(@chunks, $seq); } elsif( ($seq) = ( $line =~ /^\s*(\w+)<\/ASSEMBLY_SEQUENCE>\s*$/o) ) { push(@chunks, $seq); $self->{_assembly}->{seq} = join('', @chunks); return; } } while( $line ); $self->throw("Reached end of _proces_assembly");
}
_process_coordset($)descriptionprevnextTop
sub _process_coordset($) {
	my ($self) = @_;
	my $line;
	my $h;

	$line = $self->_readline();
	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		$line = $self->_readtag();
		($h->{end5}, $h->{end3}) = ($line =~ /<COORDSET>\s*<END5>\s*(\d+)\s*<\/END5>\s*<END3>\s*(\d+)\s*<\/END3>/os);
		if(!defined($h->{end5}) or !defined($h->{end3})) {
			$self->throw("Invalid <COORDSET>: $line");
		}
		return $h;
	} else {
		$self->throw("Bio::SeqIO::tigr::_process_coordset() called ",
		             "but no <COORDSET> found in stream");
	}
}
_process_headerdescriptionprevnextTop
sub _process_header {
	my ($self) = @_;
	my $line = $self->_readline();

	if($line !~ /<HEADER>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_header called ",
		             "but no <HEADER> found in stream");
	}

	$line = $self->_readtag();
	if($line =~ /<CLONE_NAME>([^>]+)<\/CLONE_NAME>/o) {
		$self->{_assembly}->{clone_name} = $1;
		$line = $self->_readtag();
	} else {
		$self->throw("Required <CLONE_NAME> missing");
	}

	if($line =~ /<SEQ_LAST_TOUCHED>/o) {
		# Ignored for now
$line = $self->_readtag(); } else { $self->throw("Reqired <SEQ_LAST_TOUCHED> missing"); } if($line =~ /<GB_ACCESSION>([^<]*)<\/GB_ACCESSION>/o) { $self->{_assembly}->{gb} = $1; $line = $self->_readtag(); } else { $self->throw("Required <GB_ACCESSION> missing"); } if($line =~ /<ORGANISM>\s*(.+)\s*<\/ORGANISM>/o) { my( $genus, $species, @ss ) = split(/\s+/o, $1); $self->{_assembly}->{species} = Bio::Species->new(); $self->{_assembly}->{species}->genus($genus); $self->{_assembly}->{species}->species($species); $self->{_assembly}->{species}->sub_species(join(' ', @ss)) if scalar(@ss) > 0; $line = $self->_readtag(); } else { $self->throw("Required <ORGANISM> missing"); } if($line =~ /<LINEAGE>([^<]*)<\/LINEAGE>/o) { $self->{_assembly}->{species}->classification( $self->{_assembly}->{species}->species(), reverse(split(/\s*;\s*/o, $1)) ); $line = $self->_readtag(); } else { $self->throw("Required <LINEAGE> missing"); } if($line =~ /<SEQ_GROUP>([^<]*)<\/SEQ_GROUP>/o) { # ingnored
$line = $self->_readtag(); } else { $self->throw("Required <SEQ_GROUP> missing"); } while($line =~ /<KEYWORDS>[^<]*<\/KEYWORDS>/o) { push(@{$self->{_assembly}->{keywords}}, $1); $line = $self->_readtag(); } while($line =~ /<GB_DESCRIPTION>([^<]+)<\/GB_DESCRIPTION>/o) { push(@{$self->{_assembly}->{gb_desc}},$1); $line = $self->_readtag(); } while($line =~ /<GB_COMMENT>([^<]+)<\/GB_COMMENT>/o) { push(@{$self->{_assembly}->{gb_comment}}, $1); $line = $self->_readtag(); } if(my %h = ($line =~ /<AUTHOR_LIST(?:\s*(\w+)\s*=\s*"([^"]+)"\s*)*>/o)) { #$header->{'AUTHOR_LIST'}=$h{'CONTACT'};
# Ignored
while($line !~ /<\/AUTHOR_LIST>/o) { $self->_readtag(); } $line = $self->_readline(); } else { $self->throw("Required <AUTHOR_LIST> missing"); } if($line =~ /<\/HEADER>/o) { return; } $self->throw("Reached end of header\n");
}
_process_gene_listdescriptionprevnextTop
sub _process_gene_list {
	my($self) = @_;
	my $line;

	$line = $self->_readline();
	if($line !~ /<GENE_LIST>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_gene_list called ",
		             "but no <GENE_LIST> in the stream");
	}

	$line = $self->_readline();
	if($line =~ /<PROTEIN_CODING>/o) {
		$self->_pushback($line);
		$self->_process_protein_coding();
		$line = $self->_readline();
	} else {
		$self->throw("Required <PROTEIN_CODING> missing");
	}

	if($line =~ /<RNA_GENES>/o) {
		$self->_pushback($line);
		$self->_process_rna_genes();
		$line = $self->_readline();
	} else {
		$self->throw("Required <RNA_GENES> missing");
	}

	if($line =~ /<\/GENE_LIST>/o) {
		return;
	}

	$self->throw("Reached end of _process_gene_list");
}
_process_protein_codingdescriptionprevnextTop
sub _process_protein_coding {
	my ($self) = @_;
	my $line = $self->_readline();

	if($line !~ /<PROTEIN_CODING>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_protein_coding called"
		             . "but no <GENE_LIST> in the stream");
	}

	$line = $self->_readline();
	while($line and $line =~ /<TU>/o) {
		$self->_pushback($line);
		$self->_process_tu();
		$line = $self->_readline();
	}

	# Sort the sequences
@{$self->{_sequences}} = sort { my($one, $two) = ( $a, $b ); ($one) = grep { $_->primary_tag() eq 'source' } $one->get_SeqFeatures(); ($two) = grep { $_->primary_tag() eq 'source' } $two->get_SeqFeatures(); return 0 unless defined $one and defined $two; ($one) = sort { $a <=> $b } $one->get_tagset_values(qw/end5 end3/); ($two) = sort { $a <=> $b } $two->get_tagset_values(qw/end5 end3/); return $one <=> $two; } @{$self->{_sequences}}; if($line =~ /<\/PROTEIN_CODING>/o) { return; } $self->throw("Reached end of _process_protein_coding");
}
_process_rna_genesdescriptionprevnextTop
sub _process_rna_genes {
	my ($self) = @_;
	my $line = $self->_readline();

	if($line =~ /<RNA_GENES>/o) {
		while($line !~ /<\/RNA_GENES>/o) {
			$line = $self->_readline();
		}
	} else {
		$self->throw("Bio::SeqIO::tigr::_process_rna_genes called ",
		             "but no <RNA_GENES> in the stream");
	}
}
_process_misc_infodescriptionprevnextTop
sub _process_misc_info {
	my ($self) = @_;
	my $line = $self->_readline();

	if($line =~ /<MISC_INFO>/o) {
		while($line !~ /<\/MISC_INFO>/o) {
			$line = $self->_readline();
		}
	} else {
		$self->throw("Bio::SeqIO::tigr::_process_misc_info called ",
		             "but no <MISC_INFO> in the stream");
	}
}
_process_repeat_listdescriptionprevnextTop
sub _process_repeat_list {
	my ($self) = @_;
	my $line = $self->_readline();

	if($line =~ /<REPEAT_LIST>/o) {
		while($line !~ /<\/REPEAT_LIST>/o) {
			$line = $self->_readline();
		}
	} else {
		$self->throw("Bio::SeqIO::tigr::_process_repeat_list called ",
		             "but no <MISC_INFO> in the stream");
	}
}
_process_tiling_pathdescriptionprevnextTop
sub _process_tiling_path {
	my($self) = @_;
	my $line = $self->_readline();


	if($line =~ /<TILING_PATH>/o) {
		while($line !~ /<\/TILING_PATH>/o) {
			$line = $self->_readline();
		}
	} else {
		$self->throw("Bio::SeqIO::tigr::_process_repeat_list called ",
		             "but no <MISC_INFO> in the stream");
	}
}
_process_scaffolddescriptionprevnextTop
sub _process_scaffold {
	my ($self) = @_;
	my $line;

	# for now we just skip them
$line = $self->_readline(); return if $line !~ /<SCAFFOLD>/o; do { $line = $self->_readline(); } while(defined($line) && $line !~ /<\/SCAFFOLD>/o);
}
_process_tudescriptionprevnextTop
sub _process_tu {
	my($self) = @_;
	my $line = $self->_readline();

	try {
		my $tu = Bio::Seq::RichSeq->new(-strand => 1);
		$tu->species( $self->{_assembly}->{species} );

		# Add the source tag, so we can add the GO annotations to it
$tu->add_SeqFeature(Bio::SeqFeature::Generic->new(-source_tag => 'TIGR', -primary_tag => 'source')); if($line !~ /<TU>/o) { $self->throw("Process_tu called when no <TU> tag"); } $line = $self->_readtag(); if ($line =~ /<FEAT_NAME>([\w\.]+)<\/FEAT_NAME>/o) { $tu->accession_number($1); $tu->add_secondary_accession($1); $line = $self->_readtag(); } else { $self->throw("Invalid Feat_Name"); } while($line =~ /<GENE_SYNONYM>/o) { # ignore
$line = $self->_readtag(); } while($line =~ /<CHROMO_LINK>\s*([\w\.]+)\s*<\/CHROMO_LINK>/o) { $tu->add_secondary_accession($1); $line = $self->_readtag(); } if ($line =~ /<DATE>([^>]*)<\/DATE>/o) { $tu->add_date($1) if $1 and $1 !~ /^\s*$/o; $line = $self->_readline(); } else { #$self->throw("Invalid Date: $line");
} if ($line =~ /<GENE_INFO>/o) { $self->_pushback($line); $self->_process_gene_info($tu); $line = $self->_readline(); } else { $self->throw("Invalid Gene_Info"); } my $source; my $end5; my $end3; if($line =~ /<COORDSET>/o) { $self->_pushback($line); my $cs = $self->_process_coordset(); $end5 = $cs->{end5}; $end3 = $cs->{end3}; my $length = $end3 - $end5; my $strand = $length <=> 0; $length = $length * $strand; $length++; # Correct for starting at 1, not 0
# Add X filler sequence
$tu->seq('X' x $length); # Get the source tag:
my($source) = grep { $_->primary_tag() eq 'source' } $tu->get_SeqFeatures(); # Set the start and end values
$source->start(1); $source->end($length); $source->strand(1); # Add a bunch of tags to it
$source->add_tag_value(clone => $self->{_assembly}->{clone}); $source->add_tag_value(clone_name => $self->{_assembly}->{clone_name}); $source->add_tag_value(end5 => $end5); $source->add_tag_value(end3 => $end3); $source->add_tag_value(chromosome => $self->{_assembly}->{chromosome}); $source->add_tag_value(strand => ( $strand == 1 ? 'positive' : 'negative' )); $line = $self->_readline(); } else { $self->throw("Invalid Coordset"); } if($line =~ /<MODEL[^>]*>/o) { do { $self->_pushback($line); $self->_process_model($tu, $end5, $end3); $line = $self->_readline(); } while($line =~ /<MODEL[^>]*>/o); $self->_pushback($line); $line = $self->_readtag(); } else { $self->throw("Expected <MODEL> not found"); } if($line =~ /<TRANSCRIPT_SEQUENCE>/o) { my @chunks; $line = $self->_readline(); while ($line =~ /^\s*([ACGT]+)\s*$/o) { push( @chunks, $1 ); $line = $self->_readline(); } # $line = $self->_readline();
} if($line =~ /<GENE_EVIDENCE>/o) { $line = $self->_readtag(); } while($line =~ /<URL[^>]*>[^<]*<\/URL>/o) { $line = $self->_readtag(); } if($line =~ /<\/TU>/o) { push(@{$self->{_sequences}}, $tu); return; } else { $self->throw("Expected </TU> not found: $line"); } } catch Bio::Root::OutOfRange with { my $E = shift; $self->warn(sprintf("One sub location of a sequence is invalid near line $.\: %s", $E->text())); $line = $self->_readline() until $line =~ /<\/TU>/o; return; };
}
_process_gene_infodescriptionprevnextTop
sub _process_gene_info {
	my($self, $tu) = @_;
	my $line = $self->_readline();

	$self->throw("Invalid Gene Info: $line") if $line !~ /<GENE_INFO>/o;
	$line = $self->_readline();

	if($line =~ /<LOCUS>\s*([\w\.]+)\s*<\/LOCUS>/o) {
		$tu->accession_number($1);
		$tu->add_secondary_accession($1);
		$line = $self->_readline();
	} elsif( $line =~ /<LOCUS>.*<\/LOCUS>/o) {
		# We should throw an error, but TIGR doesn't alwasy play
# nice with adhering to their dtd
$line = $self->_readtag(); } else { #$self->throw("Invalid Locus: $line");
} if($line =~ /<ALT_LOCUS>\s*([\w\.]+)\s*<\/ALT_LOCUS>/o) { $tu->accession_number($1); $tu->add_secondary_accession($1); $line = $self->_readline(); } if($line =~ /<PUB_LOCUS>\s*([\w\.]+)\s*<\/PUB_LOCUS>/o) { $tu->accession_number($1); $tu->add_secondary_accession($1); $line = $self->_readtag(); } elsif( $line =~ /<PUB_LOCUS>.*<\/PUB_LOCUS>/o) { $line = $self->_readtag(); # $self->throw("Invalid Pub_Locus");
} if($line =~ /<GENE_NAME.*>.*<\/GENE_NAME>/o) { # Skip the GENE_NAME
$line = $self->_readtag(); } if(my($attr, $value) = ($line =~ /<COM_NAME([^>]*)>([^>]+)<\/COM_NAME>/o)) { #%attribs = ($attr =~ /(\w+)\s*=\s+"(.*?)"/og);
#$geneinfo->{'CURATED'} = $attribs{CURATED};
#$geneinfo->{IS_PRIMARY} = $attribs{IS_PRIMARY}
# TODO: add a tag on sources for curated
$tu->desc($value); $line = $self->_readtag(); } else { $self->throw("invalid com_name: $line"); } while($line =~ /<COMMENT>([^<]+)<\/COMMENT>/o) { my $comment = Bio::Annotation::Comment->new( -text => $1 ); $tu->annotation()->add_Annotation('comment', $comment); $line = $self->_readtag(); } while($line =~ /<PUB_COMMENT>([^<]+)<\/PUB_COMMENT>/o) { my $comment = Bio::Annotation::Comment->new( -text => $1 ); $tu->annotation()->add_Annotation('comment', $comment); $line = $self->_readtag(); } if($line =~ /<EC_NUM>([\w\-\\\.]+)<\/EC_NUM>/o) { #$geneinfo->{'EC_NUM'} = $1;
$line = $self->_readtag(); } if($line =~ /<GENE_SYM>\s*([^<]+)\s*<\/GENE_SYM>/o) { #$tu->add_secondary_accession($1);
$line = $self->_readtag(); } if($line =~ /<IS_PSEUDOGENE>([^>]+)<\/IS_PSEUDOGENE>/o) { #$geneinfo->{'IS_PSEUDOGENE'} = $1;
$line = $self->_readtag(); } else { $self->throw("invalid is_pseudogene: $line"); } if($line =~ /<FUNCT_ANNOT_EVIDENCE/o) { $line = $self->_readtag(); } if($line =~ /<DATE>([^>]+)<\/DATE>/o) { #$geneinfo->{'DATE'} = $1;
$line = $self->_readtag(); } while($line =~ /<GENE_ONTOLOGY>/o) { # Get the source tag
my($source) = grep { $_->primary_tag() eq 'source' } $tu->get_SeqFeatures(); my @ids = ( $line =~ /(<GO_ID.*?<\/GO_ID>)/gso); foreach my $go (@ids) { my($assignment) = ($go =~ /<GO_ID\s+ASSIGNMENT\s+=\s+"GO:(\d+)">/os); my($term) = ($go =~ /<GO_TERM>([^<]+)<\/GO_TERM>/os); my($type) = ($go =~ /<GO_TYPE>([^<]+)<\/GO_TYPE>/os); # TODO: Add GO annotation
if(defined $type and defined $assignment and defined $term) { # Add the GO Annotation
$source->add_tag_value( GO => "ID: $assignment; Type: $type; $term" ); } } $line = $self->_readtag(); } if($line =~ /<\/GENE_INFO/o) { return; } $self->throw("unexpected end of gene_info");
}
_build_locationdescriptionprevnextTop
sub _build_location {
	my($self, $end5, $end3, $length, $cs) = @_;
	
	# Find the start and end of the location
# relative to the sequence.
my $start = abs( $end5 - $cs->{end5} ) + 1; my $end = abs( $end5 - $cs->{end3} ) + 1; # Do some bounds checking:
if( $start < 1 ) { throw Bio::Root::OutOfRange( -text => "locations' start( $start) must be >= 1" ); } elsif( $end > $length ) { throw Bio::Root::OutOfRange( -text => "locations' end( $end ) must be <= length( $length )" ); } elsif( $start > $end ) { throw Bio::Root::OutOfRange( -text => "locations' start ( $start ) must be < end ( $end ) $end5, $end3, $cs->{end5}, $cs->{end3}" ); } return Bio::Location::Simple->new( -start => $start, -end => $end, -strand => 1 );
}
_process_modeldescriptionprevnextTop
sub _process_model {
	my($self, $tu, $end5, $end3) = @_;
	my $line;
	my( $source ) = grep { $_->primary_tag() eq 'source' } $tu->get_SeqFeatures();
	my $model = Bio::SeqFeature::Generic->new(
		-source_tag  => 'TIGR',
		-primary_tag => 'MODEL',
	);

	$line = $self->_readline();
	if($line !~ /<MODEL ([^>]+)>/o) {
		$self->throw("Invalid Model: $line")
	}
	my %attribs = ($1 =~ /(\w+)\s*=\s*"([^"]*)"/og);
	#$model->{'CURATED'} = $attribs{'CURATED'};
# TODO: Add tag to model
$line = $self->_readline(); if($line =~ /<FEAT_NAME>\s*([\w\.]+)\s*<\/FEAT_NAME>/o) { $model->add_tag_value( feat_name => $1 ); $tu->add_secondary_accession($1); $line = $self->_readline(); } else { $self->throw("Invalid Feature Name: $line"); } if($line =~ /<PUB_LOCUS>\s*([\w\.]+)\s*<\/PUB_LOCUS>/o) { $model->add_tag_value( pub_locus => $1 ); $tu->add_secondary_accession($1); $line = $self->_readline(); } else { # $self->throw("Invalid Pub_Locus: $line");
} if($line =~ /<CDNA_SUPPORT>/o) { $self->_pushback($line); $self->_process_cdna_support( $model ); $line = $self->_readline(); } while($line =~ /<CHROMO_LINK>([^>]+)<\/CHROMO_LINK>/o) { $model->add_tag_value( chromo_link => $1 ); $line = $self->_readline(); } if($line =~ /<DATE>([^>]+)<\/DATE>/o) { $line = $self->_readline(); } else { $self->throw("Invalid Date: $line"); } if($line =~ /<COORDSET>/o) { $self->_pushback($line); my $cs = $self->_process_coordset(); my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs); $model->start( $loc->start() ); $model->end( $loc->end() ); $line = $self->_readline(); } else { $self->throw("Invalid Coordset: $line"); } my $exon = Bio::SeqFeature::Generic->new( -source_tag => 'TIGR', -primary_tag => 'EXON', -location => Bio::Location::Split->new(), -tags => [ locus => $tu->accession_number() ], ); $exon->add_tag_value( model => $model->get_tag_values('feat_name') ); my $cds = Bio::SeqFeature::Generic->new( -source_tag => 'TIGR', -primary_tag => 'CDS', -location => Bio::Location::Split->new(), -tags => [ locus => $tu->accession_number() ], ); $cds->add_tag_value( model => $model->get_tag_values('feat_name') ); my $utr = []; if($line =~ /<EXON>/o) { do { $self->_pushback($line); $self->_process_exon( $tu, $exon, $cds, $utr, $end5, $end3 ); $line = $self->_readline(); } while($line =~ /<EXON>/o); } else { $self->throw("Required <EXON> missing"); } until($line =~ /<\/MODEL>/o) { $line = $self->_readline(); } $_->add_tag_value( model => $model->get_tag_values('feat_name') ) foreach @$utr; # Add the model, EXONs, CDS, and UTRs
$tu->add_SeqFeature($model) if $model and $model->start() >= 1; $tu->add_SeqFeature($exon) if $exon and scalar($exon->location()->each_Location()) >= 1; $tu->add_SeqFeature($cds) if $cds and scalar($cds->location()->each_Location()) >= 1; $tu->add_SeqFeature(@$utr); return;
}
_process_cdna_supportdescriptionprevnextTop
sub _process_cdna_support {
	my($self, $model) = @_;
	my $line = $self->_readline();

	if($line !~ /<CDNA_SUPPORT>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_cdna_support called ",
		             "but no <CDNA_SUPPORT> in the stream");
	}

	$line = $self->_readline();

	while( $line =~ /<ACCESSION([^>]+)>(.*)<\/ACCESSION>/o) {
		# Save the text
my $desc = $2; # Get the element's attributes
my %attribs = ($1 =~ /(\w+)\s*=\s*"([^"]*)"/og); # Add the tag to the model
$model->add_tag_value( cdna_support => "DBXRef: $attribs{DBXREF}; $desc" ); $line = $self->_readline(); } if( $line =~ /<\/CDNA_SUPPORT>/o) { return; } $self->throw("reached end of _process_cdna_support");
}
_process_exondescriptionprevnextTop
sub _process_exon {
	my($self, $tu, $exon, $cds, $utr, $end5, $end3 ) = @_;
	my $line = $self->_readline();

	if($line !~ /<EXON>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_exon called ",
		             "but no <EXON> in the stream");
	}

	$line = $self->_readtag();
	if($line =~ /<FEAT_NAME>([^<]+)<\/FEAT_NAME>/o) {
		# Ignore
$line = $self->_readtag(); } else { $self->throw("Required <FEAT_NAME> missing"); } if($line =~ /<DATE>([^<]+)<\/DATE>/o) { # Ignore
$line = $self->_readtag(); } else { $self->throw("Required <DATE> missing"); } if($line =~ /<COORDSET>/o) { $self->_pushback($line); my $cs = $self->_process_coordset(); my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs); $exon->location()->add_sub_Location($loc); $line = $self->_readline(); } else { $self->throw("Required <COORDSET> missing"); } if($line =~ /<CDS>/o) { $self->_pushback($line); $self->_process_cds($tu, $end5, $end3, $cds); $line = $self->_readline(); } if($line =~ /<UTRS>/o) { $self->_pushback($line); $self->_process_utrs($tu, $end5, $end3, $utr); $line = $self->_readline(); } if($line =~ /<\/EXON>/o) { return; } $self->throw("Reached End of Bio::SeqIO::tigr::_process_exon");
}
_process_cdsdescriptionprevnextTop
sub _process_cds {
	my($self, $tu, $end5, $end3, $cds) = @_;
	my $line = $self->_readline();

	if($line !~ /<CDS>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_cda_support called ",
		             "but no <CDS> in the stream");
	}
	
	$line = $self->_readtag();
	if($line =~ /<FEAT_NAME>([^<]+)<\/FEAT_NAME>/o) {
		#$cds->{'FEAT_NAME'} = $1;
$line = $self->_readtag(); } else { $self->throw("Required <FEAT_NAME> missing"); } if($line =~ /<DATE>([^<]+)<\/DATE>/o) { #$cds->{'DATE'} = $1;
$line = $self->_readtag(); } else { $self->throw("Required <DATE> missing"); } if($line =~ /<COORDSET>/o) { $self->_pushback($line); my $cs = $self->_process_coordset(); my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs); $cds->location()->add_sub_Location($loc); $line = $self->_readline(); } else { $self->throw("Required <COORDSET> missing"); } if($line =~ /<\/CDS>/o) { return; } $self->throw("Reached onf of Bio::SeqIO::tigr::_process_cds");
}
_process_utrsdescriptionprevnextTop
sub _process_utrs {
	my($self, $tu, $end5, $end3, $utrs) = @_;
	my $line = $self->_readline();

	if($line !~ /<UTRS/o) {
		$self->throw("Bio::SeqIO::tigr::_process_utrs called but no ",
		             "<UTRS> found in stream");
	}

	$line = $self->_readline();
	while($line !~ /<\/UTRS>/o) {
		$self->_pushback($line);
		if($line =~ /<LEFT_UTR>/o) {
			$self->_process_left_utr($tu, $end5, $end3, $utrs);
		} elsif ($line =~ /<RIGHT_UTR>/o) {
			$self->_process_right_utr($tu, $end5, $end3, $utrs);
		} elsif ($line =~ /<EXTENDED_UTR>/o) {
			$self->_process_ext_utr($tu, $end5, $end3, $utrs);
		} else {
			$self->throw("Unexpected tag");
		}
	
		$line = $self->_readline();
	}

	if($line =~ /<\/UTRS>/o) {
		return $utrs;
	}
	$self->throw("Reached end of Bio::SeqIO::tigr::_process_utrs");
}
_process_left_utrdescriptionprevnextTop
sub _process_left_utr {
	my($self, $tu, $end5, $end3, $utrs) = @_;
	my $line = $self->_readline();
	my $coordset;

	if($line !~ /<LEFT_UTR>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_left_utr called but ",
		             "no <LEFT_UTR> found in stream");
	}

	$line = $self->_readtag();
	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		my $cs = $self->_process_coordset();
		my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs);

		push(@$utrs, Bio::SeqFeature::Generic->new(
		        -source_tag  => 'TIGR',
				-primary_tag => 'LEFT_UTR',
				-strand => 1,
				-start => $loc->start(),
				-end   => $loc->end()
		));

		$line = $self->_readline();
	} else {
		$self->throw("Required <COORDSET> missing");
	}

	if($line =~ /<\/LEFT_UTR>/o) {
		return;
	}
	$self->throw("Reached end of Bio::SeqIO::tigr::_process_left_utr");
}
_process_right_utrdescriptionprevnextTop
sub _process_right_utr {
	my($self, $tu, $end5, $end3, $utrs) = @_;
	my $line = $self->_readline();
	my $coordset;

	if($line !~ /<RIGHT_UTR>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_right_utr called but ",
		             "no <RIGHT_UTR> found in stream");
	}

	$line = $self->_readtag();
	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		$coordset = $self->_process_coordset();
		$self->_pushback($line);
		my $cs = $self->_process_coordset();
		my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs);

		push(@$utrs, Bio::SeqFeature::Generic->new(
		        -source_tag  => 'TIGR',
				-primary_tag => 'RIGHT_UTR',
				-strand => 1,
				-start => $loc->start(),
				-end   => $loc->end()
		));

		$line = $self->_readline();
	} else {
		$self->throw("Required <COORDSET> missing");
	}

	if($line =~ /<\/RIGHT_UTR>/o) {
		return $coordset;
	}
	$self->throw("Reached end of Bio::SeqIO::tigr::_process_right_utr");
}
_process_ext_utrdescriptionprevnextTop
sub _process_ext_utr {
	my($self, $tu, $end5, $end3, $utrs) = @_;
	my $line = $self->_readline();
	my $coordset;

	if($line !~ /<EXTENDED_UTR>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_ext_utr called but ",
		             "no <EXTENDED_UTR> found in stream");
	}

	$line = $self->_readtag();
	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		my $cs = $self->_process_coordset();
		my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs);

		push(@$utrs, Bio::SeqFeature::Generic->new(
		        -source_tag  => 'TIGR',
				-primary_tag => 'EXTENDED_UTR',
				-strand => 1,
				-start => $loc->start(),
				-end   => $loc->end()
		));

		$line = $self->_readline();
	} else {
		$self->throw("Required <COORDSET> missing");
	}

	if($line =~ /<\/EXTENDED_UTR>/o) {
		return $coordset;
	}
	$self->throw("Reached end of Bio::SeqIO::tigr::_process_ext_utr");
}
_readtagdescriptionprevnextTop
sub _readtag {
	my($self) = @_;
	my $line = $self->_readline();
	chomp($line);

	my $tag;
	if(($tag) = ($line =~ /^[^<]*<\/(\w+)/o)) {
		$self->_pushback($1) if $line =~ /<\/$tag>(.+)$/;
		return "</$tag>";
	}
 
	until(($tag) = ($line =~ /<(\w+)[^>]*>/o)) {
		$line = $self->_readline();
		chomp $line;
	}

	until($line =~ /<\/$tag>/) {
		$line .= $self->_readline();
	}

	if(my ($val) = ($line =~ /(<$tag.*>.*?<\/$tag>)/s)) {
		if($line =~ /<\/$tag>\s*(\w+[\s\w]*?)\s*$/s) {
			$self->_pushback($1)
		}
		return $val;
	}
	$self->throw("summerror");
}
_readlinedescriptionprevnextTop
sub _readline {
	my($self) = @_;
	my $line;
	do {
		$line = $self->SUPER::_readline();
	} while(defined($line) and $line =~ /^\s*$/o);

	return $line;
}
throwdescriptionprevnextTop
sub throw {
	my($self, @s) = @_;
	my $string = "[$.]" . join('', @s);
	$self->SUPER::throw($string);
}

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 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
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
the bugs and their resolution.
Bug reports can be submitted via the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORS - Josh LaurichaTop
Email: laurichj@bioinfo.ucr.edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
next_seqTop
 Title   : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : NONE