#!/usr/local/bin/perl
# parseweedxml.pl


=head1 DESCRIPTION

parseweedxml.pl -  parse tigr weed genome annotations
data at ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/PUBLICATION_RELEASE/

notes: features.tsv not yet sorted by location
 - add all useful data frm annot. xml to .tsv, then copy to weed.acode?
 - ? use revised gnomap features.tsv? with top-line == field names

=cut


$debug= 1;

use lib('/bio/work/meow/');
use POSIX;
use Getopt::Std;    

use XML::Parser; ## uses expat.c

use Meow::Data;
use Meow::Weed;
# use flybase::sym2id;

$org= 'weed';
$sourceName= 'TIGR a_thaliana/ath1/';  

$meowpub= '/bio/meow-pub/meow/server/'; #'/c3/iubio/meow-pub/meow/server/';
$genomeshome= '/c7/eugenes/genomew/'; # '/c5/tmp/genomew/';  
$tairpath= '/c7/eugenes/weed/tair/'; # oat.bio
$tigrpath= '/c7/eugenes/weed/tigr/'; # oat.bio
$outpath = '/c7/eugenes/weed/tigr/local/';  #test
$append= 1;
$outname= 'features'; # $chr.tsv
$weedids= 'ATgn'; #? $tigrpath$name or $meowpub/.etc/jdata/fbobs/$name ?
$tairGeneLocTable= $tairpath.'Gene_orf.*';

$infile= 'T9E19.xml'; ## test
$chr= '0';

# 66414454 May 10 01:55 CHR5v03172001.xml  == all Chr 5 features
# goes w/ Chr5 dna in   26718118 May 10 22:42 ATH1_pseudo_5.1con

$gnomapvers= '1';
$kMissingValue= -999999999;

$orgacode= "$meowpub/$org/acode";
$isMeowId= 1; ## for getSym2Id - acode data

@chrs= qw( 1 2 3 4 5 );
$nchr= scalar(@chrs);


%opt=();
Getopt::Std::getopts('afio:p:sxW:DA:',\%opt);

$debug= 1 if $opt{D};
$useinlist= 1 if $opt{i};
$append= 0 if $opt{a};
$mework= $opt{W} || $genomeshome; ##!!!! test, fix
$dosort= 1 if $opt{s}; # { } { }
$dorawdna= 1 if $opt{f};  

# $outpath= "$mework/$org/";  
$outpath= $opt{p} || $outpath;
$outname= $opt{o} || $outname;

unless ($useinlist || scalar(@ARGV)) {
	print "parseweedxml [-a] [-o output] [-Aacode]  xml-paths-or-files\n";
	print " converts $sourceName XML annotations to gnomap tables\n";
	print " Usage: \n -D == debug\n -a == DONT append output\n";
	print " -i == read xml file list from stdin\n";
	print " -o outname == [$outname]\n -p /output/path == [$outpath]\n";
	print " -s == sort input features.tsv by location\n";
	print " -f == convert input csome fasta seq to dna.raw \n";
#	print " -A acode == $org.acode file\n \n";
	exit;
	}

# flybase::sym2id::set4meow($isMeowId);
# flybase::sym2id::readSym2Id($orgacode, $org) if (-f $orgacode);
# ?? use tair Gene_orf.032101 for ~ 1000 matches b/n LOCUS/publocus sym and gene sym ??


unless($dosort||$dorawdna) {
	readTairGenes($tairGeneLocTable);
	$weedobj= Meow::Weed->new(); # to get id
	$weedobj->openIdDb($weedids, 'w'); #? should be 'w' but need to create
	}
	
if ($useinlist) {
	while ($infile=<>) { 
		chomp($infile);  
		die "cant read $infile" unless(-r $infile); 
		if ($dosort) { sortTable($infile); }
		elsif ($dorawdna) { fasta2raw($infile); }
		else { parseNprint( $infile); }
		}
	}
else {
	foreach $infile (@ARGV) { 
		die "cant read $infile" unless(-r $infile); 
		if ($dosort) { sortTable($infile); }
		elsif ($dorawdna) { fasta2raw($infile); }
		else { parseNprint( $infile); }
		}
	}	
$weedobj->closeIdDb() unless($dosort||$dorawdna);
	
exit;

#-------

sub fasta2raw {
	my ($fasta, $chr)= @_;
	if ($fasta =~ /\.(gz|Z)$/) { $ok= (open(FT,"gzcat $fasta|")); }
	else { $ok= (open(FT,$fasta)); }
	unless($ok) { warn "Cant read $fasta"; return; }
	
	unless($chr) { # ATH1_pseudo_4.1con
		$chr= $1 if ($fasta =~ m/ATH1_pseudo_(\d)/);
		}
	my $rawfile= "dna-$chr.raw";
		
	unless(open(OT,">$rawfile")) { warn "Cant write $rawfile"; return; }
	my ($nline, $nb);
	while(<FT>) {
		$nline++;
		if (/^>/) { warn "extra > $_" if $nline>1; next; }
		chomp();
		print OT $_;  $nb += length($_);
		}
	close(FT);  close(OT);
	warn "wrote $nb bases ($nline lines) to $rawfile from $fasta\n";
}

sub sortTable {
	my ($feattab)= @_;
	#feat sym map range id dbx notes ...
	
	my @fts= ();
	unless(open(FT,$feattab)) { warn "Cant read $feattab"; return; }
	unless(open(OT,">$feattab.sort")) { warn "Cant write $feattab.sort"; return; }
	$OUTH= *OT;
	while(<FT>) {
		unless(/^\w/) { print OT $_; next; }
		my @cols= split(/\t/); # do here or in _by_ ?
		push(@fts,\@cols);
		}
	close(FT); 
	my @sfts= sort _by_startAndGroup @fts;  
	while ($gf = shift(@sfts)) { 
   	@ft= @ $gf;
   	print OT join("\t",@ft); # printpart( @ft );
    }  
	close(OT);
}

sub _by_startAndGroup {
	my ($arange, $astart, $afeat, $agroup);
	$arange= $a->[3];
	$astart= $1 if ($arange =~ /^\D*(\d+)/); 
	$afeat= $a->[0];
	$agroup= $a->[1] || "xxx";
	# ($afeat, $agroup, $amap, $arange)= split(/\t/, $a);
	
#	if ($afeat =~ /gene/) { $seqstart{$agroup}= $astart; $arange= 1; }
#	elsif ($afeat =~ /CDS|mRNA/) { $astart= $seqstart{$agroup} || $astart; $arange= 2; }
#	else { $arange= 3; }
	if ($afeat =~ /gene/) { $arange= 1; }
	elsif ($afeat =~ /CDS|mRNA/) { $arange= 2; }
	else { $arange= 3; }

	my ($brange, $bstart, $bfeat, $bgroup);
	$brange= $b->[3];
	$bstart= $1 if ($brange =~ /^\D*(\d+)/); 
	$bfeat= $b->[0];
	$bgroup= $b->[1] || "xxx";
	
	if ($bfeat =~ /gene/) { $brange= 1; }
	elsif ($bfeat =~ /CDS|mRNA/) { $brange= 2; }
	else { $brange= 3; }
	
  $byr= ( $astart <=> $bstart );
	if ($byr == 0) {
  	$byr= ( $agroup cmp $bgroup );
  	if ($byr == 0) { $byr = ($arange <=> $brange); }
	  }
	return $byr;
}
 
sub readTairGenes {
	my ($genetab)= @_;
	my $fn= $genetab;
	unless(-r $fn) { $fn= `ls -1 $fn`; } # wild-card name?
	unless(open(TG,$fn)) { warn "Cant read $genetab"; return; }
	%loc2gsym= ();
	my($gsym, $atloc);
	while(<TG>) {
		chomp();
		($gsym, $atloc)= split(/\t/);
		$atloc= uc($atloc); # make sure of case
		$loc2gsym{$atloc}= $gsym;
		}
	close(TG);
}

sub parseNprint {
	my ( $inxml ) = @_;
	%els= ();
	%assemblyvals= ();
	
	$p2 = new XML::Parser(Handlers => 
			{Start => \&handle_start,
			 End   => \&handle_end,
			 Char  => \&handle_char,
			 # Default => \&handle_default,
			 } );
	
	if ($inxml =~ /\.(gz|Z)$/) {
		if (open(XFILE,"gzcat $inxml|")) {
			$p2->parse(*XFILE); close(XFILE);
		  }
		}
	else { $p2->parsefile($inxml); }

  close($OUTH) if ($OUTH); $OUTH= undef;

	
#	while ($gf = shift(@fts)) { # print as feat is collected ?
#	  # print STDERR "sym: ".$gf->[1]."\t range: ".$gf->[2]."\n" if ($debug);
#   	@ft= @ $gf;
#   	printpart( @ft );
#    }  

	if (1) {
	 print "Weed XML tags for $inxml\n";
	 foreach (sort keys %els) { print "$_\t$els{$_}\n"; }
	# print "Counts:\n  N gene=$ngene\n  N mrna=$nmrna\n  N annot=$nannot\n  N span=$nspan\n";
	# print "Unknown values\n";
	# foreach (sort keys %unknowns) { print "$_\t$unknowns{$_}\n"; }
	 }

}

sub openout {
	my ($infile, $chr, $chrsize, $date) = @_;
	unless($OUTH) {
		my $fname= "$outname-$chr.tsv";
		$fout= "${outpath}$fname";
		# print "dumpFeatures $fout\n" if ($debug);
		my $ok;
		if ($append && -r $fout) { $ok= open(FOUT,">>$fout"); }
		else { $ok= open(FOUT,">$fout"); }
		unless ($ok) { warn "can't write $fout"; return -1; }
		$OUTH= *FOUT;
		$append= 1; # for remaining files of same csome
		print $OUTH &feattabheader("$org/$fname",$org,$infile,$date);
		print $OUTH "source\t$org\tChr $chr\t1..$chrsize\t-\n" if $chrsize; #? get from .xml
		}
} 	

sub pushFeat {
	my @ft= @_; 
	# printpart wants: ($feat,$gsym,$range,$id,$dbxref,$note)
	if ($OUTH) { printpart( @ft ); }
	else { push( @fts, \@ft); } 
}

sub pushGene {
	my ($tutype)= @_;
		## ? COM_NAME only for RNAs ? || $vals{COM_NAME}
		## save COM_NAME , PUB_COMMENT for acode genes ?
		## $vals{GENE_SYM}  not seen in CHR4/5
		## ? PUB_COMMENT
	my ($gsym, $notes, $egid, $dbxref, $aval, $publoc, $ispred, $idval, $public, $bacloc);

	## Argh ! {PUB_LOCUS} is not a uniq id - 145 dups are found ! $vals{LOCUS} has more dups
	## !? need to use TU-FEAT_NAME id? do as tigr chr.pep fasta: id=feat-id#bacloc#publoc
	## Double Argh! different cases for PUB_LOCUS - need same case always - AT#g#####
	
	if (scalar(@ranges)<1) { warn "pushGene( $vals{PUB_LOCUS} ) - null range\n"; return; }
	my $range= makerange( \@ranges, 0);  @ranges= ();
	
	if ($tutype eq 'mRNA' || $tutype eq 'gene') { 
		# $gsym= $vals{GENE_SYM} || $vals{PUB_LOCUS} || $vals{LOCUS} ;  #? which is best
		$publoc= $vals{PUB_LOCUS};
			$publoc =~ s/At(\d)g/At$1g/i;  # ! standardize case !
			
		$bacloc= $vals{LOCUS};
		
		if ($vals{GENE_SYM}) { $gsym= $vals{GENE_SYM}; }
		elsif ($publoc) {
			my $ucloc= uc($publoc);
			if ($loc2gsym{$ucloc}) { $gsym= $loc2gsym{$ucloc}; }
			else { $gsym= $publoc;  $ispred= 1; }
			}
		else {
			$gsym= $bacloc;  # this is BAC_Locus, always there
			$ispred= 1; 
			}
		# !! using old weed data this LOCUS is prefered symbol over PUB_LOCUS (change mup24_50 to mup24.50 tho)
		# $notes .=  'BAC_Locus='.$vals{LOCUS}.' ; ';  
  	# BAC_Locus: mup24_50
  	
		$idval= $tufeatid.'#'.$bacloc.'#'.$publoc;
		# $idval= $gsym; # -- was, but NOT UNIQUE to a gene loc
		}
	
	if ($tutype eq 'mRNA') { 
		# $gsym= $vals{GENE_SYM} || $vals{PUB_LOCUS} || $vals{LOCUS} ;   
		if ($weedobj) {
			# my $cksum= $publoc; # or FEAT_NAME ? $weedobj->checksum($_); 
			$egid= $weedobj->getId($idval, $datadate, $publoc); ## reuse same id/sym
			}
		}
	elsif ($tutype =~ /RNA/) { 
		$gsym= $vals{COM_NAME};
		$notes .=  'comment='.$vals{PUB_COMMENT}.' ; ' if ($vals{PUB_COMMENT});
		}
	else { # if ($tutype eq 'gene')	
		$dbxref .=  'EC:'.$vals{EC_NUM}.' , ' if ($vals{EC_NUM}) ;
		
			# both LOCUS == BAC_Locus and PUB_LOCUS work TIGRLOC url
		  # $publoc= $vals{PUB_LOCUS} || $vals{LOCUS};
		$dbxref .=  'AGILOC:'.$publoc.' , ' if ($publoc);
		$dbxref .=  'AGIBAC:'.$bacloc.' , ' if ($bacloc); #! this is in AGR acedb Locus = BAC_Locus
		$dbxref .=  'TIGRFT:'.$tufeatid.' , ';  

		$aval= $vals{COM_NAME};
		$notes .=  'name='.$aval.' ; ' if ($aval =~ m/\w/);
		$notes .=  'pseudogene=1 ; ' if ($vals{IS_PSEUDOGENE} eq '1');
		$aval= $vals{PUB_COMMENT};
		$notes .=  'comment='.$aval.' ; ' if ($aval =~ m/\w/);
		$notes .=  'predicted=1 ; ' if ($ispred);

		# $egid= 'ATgn'.sprintf("%07d",0); # FIXME  -- dummy id, need euGenes generated one
		if ($weedobj) {
			# my $cksum= $publoc; # or FEAT_NAME ? $weedobj->checksum($_); 
			$egid= $weedobj->getId($idval, $datadate, $publoc); ## reuse same id/sym
			}
			
		}
	pushFeat( $tutype, $gsym, $range, $egid, $dbxref, $notes); #! need RNA options for this feat.
}

 
#-- start xml handler subs

# change to hash all of a TU (see TIGR parser.pl example)
# and print at end of TU (or related RNA forms)

sub handle_start {
#(Expat, Element [, Attr, Val [,...]])
	my ($expat, $elem, @atvals)= @_;
  push(@els, $inel);
  local $_= $elem;
  $inel= $_;
  $els{$_}++;
  $skipchar= 0;
  $vals{$_}= '';
  
  SWITCH: {
		/^ASSEMBLY$/ &&  do {  
			%assemblyvals= @atvals;
			# $database= $assemblyvals{DATABASE};
			# $datadate= $assemblyvals{CURRENT_DATE};
			# $chr= $assemblyvals{CHROMOSOME};
			last SWITCH; };   

		/^GENE_LIST$/ &&  do { %vals= (); last SWITCH; };  
		
			# collect all in hash{}{}{} from here?
		/^PROTEIN_CODING$/ &&  do { $tutype= 'gene'; $tufeatid= ''; %vals= (); last SWITCH; };  
		/^RNA_GENES$/ &&  do {  $tutype= 'RNA'; %vals= (); last SWITCH; };  
		/^RRNA$/ &&  do {  $tutype= 'rRNA'; %vals= (); last SWITCH; };  
		/^SNRNA$/ &&  do {  $tutype= 'snRNA'; %vals= (); last SWITCH; };  
		/^SNORNA$/ &&  do {  $tutype= 'snoRNA'; %vals= (); last SWITCH; };  
		/^PRE-TRNA$/ &&  do {  $tutype= 'tRNA'; $tufeatid= ''; %vals= (); last SWITCH; };  
		
		/^TU$/ &&  do { %vals= (); $tufeatid= ''; @ranges= ();  last SWITCH; };   
		
		/^MODEL$/ &&  do { # |TRNA 
			pushGene($tutype); # $tutype  TU end or MODEL start?
			# push(@rangeset, \@ranges);  @ranges= (); # save gene @ranges
			last SWITCH; };  

		/^END5$/ &&  do { $start= '';  last SWITCH; }; 
		/^END3$/ &&  do { $stop= '';  last SWITCH; }; 
			
#		/^EXON$/ &&  do { last SWITCH; };   
#		/^GENE_INFO$/ &&  do { last SWITCH; };   
#		/^COORDSET$/ &&  do { last SWITCH; };    
#		/^FEAT_NAME$/ &&  do {  last SWITCH; };  
#		/^LOCUS$/ &&  do {  last SWITCH; };  
#		/^PUB_LOCUS$/ &&  do {  last SWITCH; };   
#		/^GENE_SYM$/ &&  do {  last SWITCH; };  
#		/^EC_NUM$/ &&  do {  last SWITCH; };  
#		/^IS_PSEUDOGENE$/ &&  do {  last SWITCH; };  
#		/^REPEAT$/ &&  do {  last SWITCH; };   
#		/^REPEAT_TYPE$/ &&  do {  last SWITCH; };  
		$nada= 1;
		}
  
#  if ($addxpath) {
#  	# $ar= $xpath->{$inel};
#  	# if (ref($ar) =~ /ARRAY/) $na= $ar->
#  	}

}


sub handle_end {
#(Expat, Element)
	my ($expat, $elem)= @_;
	warn "end: $elem <> $inel inel\n" if ($elem ne $inel);
	$inel= pop(@els); #== one above current $elem
  local $_= $elem;
  SWITCH: {

 		/^HEADER$/ &&  do { 
			$database= $assemblyvals{DATABASE};
 			$datadate= $assemblyvals{CURRENT_DATE};
			$chr= $assemblyvals{CHROMOSOME};
			$chrsize= $sourcerange[1];
			openout( $infile, $chr, $chrsize, $datadate);
 			last SWITCH; };  

#		/^GENE_LIST$/ &&  do { last SWITCH; };   
#		/^RNA_GENES$/ &&  do { last SWITCH; };   
#		/^PROTEIN_CODING$/ &&  do { last SWITCH; };   
			
		/^TU$/ &&  do { 
			# pushGene($tutype); # TU end or MODEL start?
			last SWITCH; }; 
			
		/^MODEL$/ &&  do { 
			pushGene('mRNA');
#			$range= makerange( \@ranges, 0);  $rref= pop(@rangeset); @ranges= @$rref;  
#			$gsym= $vals{GENE_SYM} || $vals{PUB_LOCUS} || $vals{LOCUS} ; #? which is best
#			# $id= ???  
#			pushFeat('mRNA',$gsym,$range);
			last SWITCH; };  

	  /^(SNORNA|RRNA|SNRNA)$/ &&  do { 
			pushGene($tutype);
			last SWITCH; };  

		/^TRNA$/ &&  do { 
			pushGene('tRNA');  
			last SWITCH; }; 
					
#		/^EXON$/ &&  do { last SWITCH; };  
#		/^GENE_INFO$/ &&  do { last SWITCH; };   
			
		/^END5$/ &&  do { $rstart= $vals{$_};  last SWITCH; }; 
		/^END3$/ &&  do { $rstop = $vals{$_};  last SWITCH; };  
		
		/^COORDSET$/ &&  do { 
				$getrange= ($inel =~ /^(EXON|TU|REPEAT|TRNA|SNORNA|SNRNA|RRNA|ASSEMBLY)$/); 	
					# |RNA-EXON  |PRE-TRNA == mRNA or gene ?
				if ($getrange) {
				if ($rstart>$rstop) { $rng= "$rstop..$rstart"; $compl= 1; }
				else { $rng= "$rstart..$rstop";  $compl= 0; }
				if ($inel =~ /ASSEMBLY/) { @sourcerange= ($rstart, $rstop); }
				else { push(@ranges, $rng) ; }
				}
				last SWITCH; };   

 		/^FEAT_NAME$/ &&  do { 
			if ($inel =~ /^(TU|PRE-TRNA)$/) { $tufeatid= $vals{$_}; }
 			last SWITCH; }; 

#		/^LOCUS$/ &&  do {   last SWITCH; };  
#		/^PUB_LOCUS$/ &&  do {  last SWITCH; };  
#		/^GENE_SYM$/ &&  do {  last SWITCH; }; 
#		/^EC_NUM$/ &&  do {  last SWITCH; };  
#		/^IS_PSEUDOGENE$/ &&  do {  last SWITCH; }; 

#		/^REPEAT_TYPE$/ &&  do {  last SWITCH; }; 
		/^REPEAT$/ &&  do {  
			$range= makerange( \@ranges, 0);  @ranges= ();
			$featname= $vals{REPEAT_TYPE};  
			pushFeat('repeat',$vals{REPEAT_TYPE},$range);
			last SWITCH; };  
			
		$nada= 1;
		}
  
}

sub handle_char {
#(Expat, String)
  return if ($skipchar);
	my ($expat, $val)= @_;
	$vals{$inel} .= $val;
  # $xpath->{$inel} .= $val if ($xpath);
  # $xpath->{$inel}->[0]->{content} .= $val if ($xpath);
}

sub handle_default {
#(Expat, String)
	my ($expat, $val)= @_;
}

#-- end xml parse


sub feattabheader {
  my ($fname,$org,$sourcefile, $date)= @_;
	
	unless($date) {
		my @tm= localtime( $^T - 24*60*60*(-M $sourcefile) );
		$date= POSIX::strftime("%d-%B-%Y",@tm);
		}
		
	$sourcefile =~ s|^$genomeshome||;
	$sourcefile =~ s|^$tigrpath||;
	$sourcefile =~ s|^$tairpath||;
	
	return <<EOF;
\# $fname
\# Features for $org from $sourceName [ $sourcefile, $date]
\# gnomap-version $gnomapvers
\#
\# tab-separated-values
\# Feature	gene 	map 	range 	id	db_xref  	notes

EOF
}



sub printpart {
	my ($feat,$gsym,$range,$id,$dbxref,$note)= @_;	
	## $range= 'complement('.$range.')' if ($compl eq '-');
	$dbxref= '-' unless($dbxref);
	$gsym= '-' unless($gsym);
	$note= '-' unless($note);
	$id= '-' unless($id);

#	my $dock= 0;
#	if ($gsym ne '-') {
##	  if ($id !~ /\d/) { $dock= 1; }
##		elsif ($feat eq 'gene' && flybase::sym2id::id2symbol($id) ne $gsym) { $dock= 1; }
#			## ^^ do this even if have $id - can be 2ndary ID or old sym !
#		}
#	if ($dock) {
##		$id= flybase::sym2id::symbol2id($gsym) || $id; ## $sym2id{ symcase($gsym) } || $id; ### or '-'?
##		$gsym= flybase::sym2id::id2symbol($id) || $gsym; # make sure is proper symbol
#		}
	$dbxref =~ s/[\n\r]/ /g;
	$note =~ s/[\n\r]/ /g;
	print $OUTH "$feat\t$gsym\t-\t$range\t$id\t$dbxref\t$note\n";
}

sub makerange {
	my ($aref, $domax)= @_;
	my @ra= @$aref;
	my $rng;
		#? need to sort ranges numerically? - YES, for $compl at least
		# given order of spans is from start of gene/mRNA to end, even if from top to bottom?
	if ($compl) {
		for (my $i= $#ra; $i>=0; $i--) {
			$_= $ra[$i];  next unless($_); ##?
			if ($rng) { $rng .= ",$_"; } else { $rng= $_; }
			}
		}
	else {
		foreach (@ra) {
			next unless($_); ##?
			if ($rng) { $rng .= ",$_"; } else { $rng= $_; }
			}
		}
	if ($domax) { my($start,$stop)= maxrange($rng); $rng= "$start..$stop"; }
	$rng= 'join('.$rng.')' if ($rng =~ /,/);
	$rng= 'complement('.$rng.')' if ($compl); 
	return $rng;
}

sub maxrange {
	my( $range)= @_;
	my ($pre, $suf,$start,$stop, $b, $u);
	$start= $kMissingValue; $stop= $start;
	
	$range =~ s/^([^\d<>-]*)//; $pre= $1;
	$range =~ s/(\D*)$//;  $suf= $1;
	if ($range =~ m/^([<>]*)([\d-]+)/) { $u= $1; $start= $2; $start-- if ($u eq '<'); }
	if ($range =~ m/([<>]*)([\d-]+)$/) { $u= $1; $stop= $2; $stop++ if ($u eq '>'); }
	return ($start,$stop);
}

__END__


tigrxml.dtd tags we want

 <ASSEMBLY CLONE_ID = "0" DATABASE = "ATH1" CHROMOSOME = "5" CURRENT_DATE = "Wed May  2 09:16:00 EDT 2001">
                        <ASMBL_ID>68197</ASMBL_ID>
                        <COORDSET>
                                <END5>1</END5>
                                <END3>26280090</END3>
                        </COORDSET>
                        <HEADER>


<!ELEMENT GENE_LIST (PROTEIN_CODING, RNA_GENES)>
<!ELEMENT RNA_GENES (PRE-TRNA*, SNRNA*, SNORNA*, RRNA*) >
<!ELEMENT FEAT_NAME (#PCDATA) > -- LOCUS or PUB_LOCUS

<!ELEMENT PROTEIN_CODING (TU*) >
<!ELEMENT TU (FEAT_NAME, DATE, GENE_INFO, COORDSET, MODEL+, TRANSCRIPT_SEQUENCE) >
<!ELEMENT MODEL (FEAT_NAME, DATE, COORDSET, EXON+, CDS_SEQUENCE?, PROTEIN_SEQUENCE?) >
<!ATTLIST MODEL COMMENT          CDATA      #IMPLIED >

<!ELEMENT EXON (FEAT_NAME, DATE, COORDSET, CDS?, UTRS?) >

<!ELEMENT CDS  (FEAT_NAME, DATE, COORDSET) >

# this is 1-based, if END5 > END3, the negative strand
<!ELEMENT COORDSET (END5, END3) >
<!ELEMENT END5 (#PCDATA)>
<!ELEMENT END3 (#PCDATA)>


<!ELEMENT GENE_INFO (LOCUS, PUB_LOCUS?, COM_NAME, PUB_COMMENT?, EC_NUM?, GENE_SYM?, IS_PSEUDOGENE, DATE, ROLE_LIST?, EVIDENCE?) >

<!ELEMENT LOCUS (#PCDATA) >   -- BAC id
<!ELEMENT PUB_LOCUS (#PCDATA) >  -- publication/true name
<!ELEMENT COM_NAME (#PCDATA) >
<!ELEMENT PUB_COMMENT (#PCDATA) >
<!ELEMENT EC_NUM (#PCDATA) >
<!ELEMENT GENE_SYM (#PCDATA) >  -- gene symbol
<!ELEMENT IS_PSEUDOGENE (#PCDATA) > -- {1=true|0=false}



<!ELEMENT REPEAT_LIST (REPEAT*) >
<!ELEMENT REPEAT (FEAT_NAME, DATE, COORDSET, REPEAT_TYPE) >
<!ELEMENT REPEAT_TYPE (#PCDATA) >

<!ELEMENT RRNA (FEAT_NAME, DATE, COORDSET, COM_NAME) >
<!ELEMENT SNRNA (FEAT_NAME, DATE, COORDSET, COM_NAME) >
<!ELEMENT SNORNA (FEAT_NAME, DATE, COORDSET, COM_NAME) >


--        PRE-TRNA ~ TU  , TRNA ~ MODEL , RNA-EXON ~ EXON

<!ELEMENT PRE-TRNA (FEAT_NAME, DATE, COORDSET, TRNA) >
<!ELEMENT TRNA (FEAT_NAME, DATE, COORDSET, COM_NAME, RNA-EXON+) >
<!ATTLIST TRNA ANTICODON         NMTOKEN    #REQUIRED >
<!ELEMENT RNA-EXON (FEAT_NAME, DATE, COORDSET)>


-- function info, (gene ontology), etc
<!ELEMENT ROLE_LIST (ROLE_INFO+) >

<!ELEMENT ROLE_INFO (COMPARTMENT, DATE, MAIN_ROLE,  SUBROLE_1?, SUBROLE_2?, SUBROLE_3?, SUBROLE_4?) >
<!ELEMENT COMPARTMENT (#PCDATA) >
<!ELEMENT MAIN_ROLE (#PCDATA) >
<!ELEMENT SUBROLE_1 (#PCDATA) >
<!ELEMENT SUBROLE_2 (#PCDATA) >
<!ELEMENT SUBROLE_3 (#PCDATA) >
<!ELEMENT SUBROLE_4 (#PCDATA) >

??
<!ELEMENT EVIDENCE EMPTY >
<!ATTLIST EVIDENCE GENE_PREDICTIONS NMTOKEN #REQUIRED>
<!ATTLIST EVIDENCE PROTEIN_MATCHES NMTOKEN #REQUIRED >
<!ATTLIST EVIDENCE GENE_INDEX_MATCHES NMTOKEN #REQUIRED >

..

                      <RNA_GENES>
                        </RNA_GENES>
                </GENE_LIST>
                <REPEAT_LIST>
                        <REPEAT>
                                <FEAT_NAME>67977.repeat00001</FEAT_NAME>
                                <DATE>Feb  7 2001  7:42AM</DATE>
                                <COORDSET>
                                        <END5>17839</END5>
                                        <END3>17814</END3>
                                </COORDSET>
                                <REPEAT_TYPE>AT_rich</REPEAT_TYPE>
                        </REPEAT>
                </REPEAT_LIST>


                                <PRE-TRNA>
                                        <FEAT_NAME>68071.pre&#x2D;tRNA&#x2D;Ile&
#x2D;1</FEAT_NAME>
                                        <DATE>Sep 21 2000  1:14AM</DATE>
                                        <COORDSET>
                                                <END5>105712</END5>
                                                <END3>105639</END3>
                                        </COORDSET>
                                        <TRNA ANTICODON = "TAT">
                                                <FEAT_NAME>68071.tRNA&#x2D;Ile&#
x2D;1</FEAT_NAME>
                                                <DATE>Sep 21 2000  1:14AM</DATE>
                                                <COORDSET>
                                                        <END5>105712</END5>
                                                        <END3>105639</END3>
                                                </COORDSET>
                                                <COM_NAME>tRNA&#x2D;Ile</COM_NAM
E>
                                                <RNA-EXON>
                                                        <FEAT_NAME>68071.x00001<
/FEAT_NAME>
                                                        <DATE>Sep 21 2000  1:14A
M</DATE>
                                                        <COORDSET>
                                                                <END5>105712</EN
D5>
                                                                <END3>105639</EN
D3>
                                                        </COORDSET>
                                                </RNA-EXON>
                                        </TRNA>
                                </PRE-TRNA>

>> ?? NO repeats in the pseudochromosomes ??

oat% ./parsewe* CHR5v03172001.xml
dumpFeatures /c7/eugenes/weed/tigr/features-5.tsv
Weed XML tags
ASMBL_ID        409
ASMBL_LEFT_COORD        408
ASMBL_RIGHT_COORD       408
ASSEMBLY        1
ASSEMBLY_SEQUENCE       1
AUTHOR_LIST     1
CDS     31063
CDS_SEQUENCE    5849
CHR_LEFT_COORD  408
CHR_RIGHT_COORD 408
CLONE_NAME      1
COM_NAME        5851
COORDSET        73838
DATE    80094
EC_NUM  661
END3    73838
END5    73838
EXON    31070
FEAT_NAME       73835
GB_ACCESSION    1
GENE_INFO       5851
GENE_LIST       1
HEADER  1
IS_PSEUDOGENE   5851
LEFT_UTR        1
LINEAGE 1
LOCUS   5851
MODEL   5851
ORGANISM        1
ORIENTATION     408
PROTEIN_CODING  1
PROTEIN_SEQUENCE        5849
PSEUDOCHROMOSOME        1
PUB_COMMENT     5738
PUB_LOCUS       5839
RIGHT_UTR       1
RNA_GENES       1
SCAFFOLD        1
SCAFFOLD_COMPONENT      408
SEQ_GROUP       1
TIGR    1
TRANSCRIPT_SEQUENCE     5851
TU      5851
UTRS    1


# weed/features-5.tsv
# Features for weed from TIGR a_thaliana/ath1/ [ CHR5v03172001.xml, Wed May  2 09:16:00 EDT 2001]
# gnomap-version 1
#
# tab-separated-values
# Feature       gene    map     range   id      db_xref         notes

source  weed    Chr 5   1..26280090     -
gene    AT5g60640       -       complement(23675728..23678580)  ATgn0000000 EC:5.3.4.1      -
mRNA    AT5g60640       -       complement(join(23675728..23675937,23676027..236

oat% more ATH1_pseudo_5.1con
>68197  , , , 26280090 bp
TATACCATGTACCCTCAACCTTAAAACCCTAAAACCTATACTATAAATCTTTAAAACCTA
TACTCTAAACCATAGGGTTTGTGAGTTTGCATAAAGCGTCACGTATAAGTGTTTCTAACA