#!/usr/local/bin/perl
# parsehumap.pl
# parse human ensembl features -- genbank format

$debug= 0;

use Getopt::Std;    
use POSIX;
use flybase::sym2id;

## paths for iubio/kalo
$meowpub= '/c6/iubio/meow-pub/meow/server/';
$genomeshome= '/c7/eugenes/genomew/';  
$humanens= '/c7/eugenes/human/ensembl/';  
$mapdir= $humanens . 'maps/';
$gbfeatdir= $humanens . 'genbank/';

$org= 'man';
$orgacode= "$meowpub/$org/acode";
$isMeowId= 1; ## for getSym2Id - acode data
$gnomapvers= '1';
$kMissingValue= -999999999;

$doprot= 0;
$wantdna= 0;
$wantfeat= 1;

$sourename= 'EnsEMBL human annotation data';

@chrs= qw( 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y Un);
# or is it 01 or CHR_01 ?

$nchr= scalar(@chrs);
$scaf= 0;

%opt=();
Getopt::Std::getopts('o:xW:DA:',\%opt);

$mework= $opt{W} || $genomeshome;  
$outpath= "$mework/$org/";  
$outpath= $opt{o} || $outpath;
$orgacode= $opt{A} if $opt{A};
$debug= 1 if $opt{D};
$featout= "$outpath/features.tsv";

unless ($opt{x} || scalar(@ARGV)) {
	print "parsehumap [-o output] [-Aacode] [-x] ensembl-gb-files\n";
	print " Usage: \n -D == debug\n -o output path == [$outpath]\n -A acode == man.acode file\n -x = use default files \n";
	exit;
	}

# ? read @ARGV for input files?

flybase::sym2id::set4meow($isMeowId);
flybase::sym2id::readSym2Id($orgacode, $org);

readcontigs();
readclones();

readfeats();

exit();
#--------

# readensgb - foreach locus(seqid)
#    foreach feature
#       featkind, featname, cmap?,  bpmap,  egID,  dbxref, notes
#       featname = ? from egID->sym map || from /gene="ENSG00000089311"
#       egID = ? from /dbxref=LOCUSLINK  
#   				also have REFSEQ,EMBL,SPTREMBL,HUGO,MIM,
#   		bpmap = reformat of location -> 
#   			flip?? 	join(complement(102579..102620),complement(102434..102574),...)
#   			 to  complement(...,join(c..d),join(a..b))
#   			add csome offset: 
#   				ctgid= clones(seqid).ctgid
#   				clones(seqid).start,len should == feat.location.start,len
#   			  + contigs(ctgid).start,len
#   			  
#   	  cmap? == CytogeneticMap

sub readfeats {
	my $dir= shift || $gbfeatdir;
	my $fout= shift || "$outpath/features-$gname.tsv";
	my $ok;
	local(*D,*FH,*FOUT,*FDNA);
	
	return "cant open $dir" unless (opendir(D,$dir));
	@fn= grep( /ensembl/, readdir(D) ); #ensembl.1000.dat.gz
	close(D);

	if ($wantfeat) {
		unless (open(FOUT,">$fout")) { warn "can't write $fout"; return -1; }
		print FOUT &feattabheader("$org/features-$gname.tsv",$org,$dir.$fn[0]);
		}
# 	if ($doprot) {
# 		$fout= "$outpath/cds-$gname.fasta";
# 		unless (open(FPROT,">$fout")) { warn "can't write $fout"; return -1; }
# 		}
# 	if ($wantdna) {
# 		$fout= "$outpath/dna-$gname.raw";
# 		unless (open(FDNA,">$fout")) { warn "can't write $fout"; return -1; }
# 		}

	foreach my $fn (sort @fn) {
		$fn = $dir . $fn;
		print STDERR "readfeat($fn)\n" if $debug;
		if ($fn =~ /\.gz/) { $ok= open(FH,"gzcat $fn|"); } else { $ok= open(FH,$fn); }
		readfeat(*FH, *FOUT, *FDNA) if ($ok);
		close(FH);
		}
	close(FOUT);
}


# from genomefeat.pl
sub feattabheader {
  my ($fname,$org,$sourcefile)= @_;
	my @tm= localtime( $^T + 24*60*60*(-M $sourcefile) );
	my $date= POSIX::strftime("%d-%B-%Y",@tm);
	$sourcefile =~ s/^$genomeshome//;
	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 readfeat {
	my ($fh, $fout, $fdna) = @_;
	my ($seqid, $infeat, $inseq, $ok, $ftname,$ncds,$nfeat, $ndna );
	my @feat= ();
	while (<$fh>) {
		my $line= $_;
		if (/^LOCUS\s+(\S+)/) { 
			$seqid= $1;
			$infeat= 0; $inseq= 0;
			}
		elsif (/^FEATURES/) { $infeat= 1; }
		elsif ($inseq && $wantdna) {
			s/\s+//g; ## no spaces
			s/\d+//g; ## eat line numbers
			$ndna += length($_);
			# print $fdna $_ if ($_);
			}
		elsif (/^(ORIGIN|CONTIG)/) { #? other end-of-feature fields?
	  	if (scalar(@feat)) {
				printFeat($fout,$org,$seqid,@feat) if ($wantfeat); $nfeat++;
		  	# $ncds += CDS2Fasta($fprot,@feat) if ($ftname eq 'CDS' && $doprot);
	  		@feat= (); 
	  		}
			$infeat= 0; 
			## opt pull sequence data into single raw file ! 
			if ($wantdna) { $inseq= 1; }
			# else { last; } ## return $ncds -- NOT last, many LOCUS per file; 
			}
		elsif ($infeat) {
		  if (/^     (\S+) /) { 
			  my $newftname= $1;
		  	if (scalar(@feat)) {  
					$nfeat++;
					printFeat($fout,$org,$seqid,@feat) if ($wantfeat); ## $species{$org} 
			  	# $ncds += CDS2Fasta(*FPROT,@feat) if ($ftname eq 'CDS' && $doprot);
		  		}
		  	$ftname= $newftname;
		  	@feat= (); push(@feat,$line);  
		  	}
		  elsif (/^              /) {
		  	push(@feat,$line);
				}
			} 
		}
}

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);
}

sub parseFeat {
	my( @feat)= @_;
	my ($featname, $srange, $fnote, $val, $map, $id, $gsym,$inrange);
	my @dbx= ();
	my %fnotes= ();
	
	my $fline= shift(@feat);
	if ($fline =~ /^     (\S+)\s+(\S+)/) { ## 1st line only !?
		$featname= $1;
		$srange= $2;
		$inrange= 1;
		# recode some featnames
		$featname= 'repeat' if ($featname eq 'repeat_region');
		}
		
	foreach (@feat) {
		if ( m|^\s+/(\w+)\s*=\s*"([^"]+)|) { 
			$fnote= $1; $val= $2;  
  		$fnotes{$fnote}++; $inrange= 0;
     
     # ens notes include 
     # /db_xref="EMBL:X07448"
     # /transcript="ENST00000004493"
     # /cds="ENSP00000004493"
     # /gene="ENSG00000003981"
     # /translation="MDWTWRILFLVAAATGAHSQVQLVQSGAEVKKPGASVKVSCKASG
  		
	 		if ($fnote eq 'gene') { $gsym= $val;} #! this is ENSG0000 if ensembl
	 		elsif ($fnote eq 'map') { $map= $val;}
	 		elsif ($fnote eq 'chromosome') {   #? only in source feature?  not in worm csome
	 			$map= "Chr $val";
	 			$chromosome= $val;
	 			}
	 			
	  	elsif ($fnote eq 'protein_id') { 
	  		if ($featname eq 'CDS') { $id= $val; }
				else { push(@dbx, "PROTID:$val"); } ##? leave out if $id
	  		}
	  	elsif ($fnote eq 'db_xref') {
	  			## FIXME parse out prime ID from here
	  		my $id1;
	  		if ($org eq 'man' && $featname eq 'CDS' && $val =~ /LOCUSLINK/) { 
	  			$id1= $val; 
	  			$id1 =~ s/LOCUSLINK://;
	  			$id1 = 'MEOW:HUgn' . sprintf("%07d",$id1);  
	  			}
	  		elsif ($org eq 'man' && $featname eq 'CDS' && $val =~ /gene/) { $id1= $val; }
# 	  		elsif ($org eq 'fly' && $featname eq 'gene' && $val =~ /FBgn/) { $id1= $val; }
# 	  		elsif ($org eq 'fly' && $featname eq 'mRNA' && $val =~ /FBan/) { $id1= $val; } 
# 	  		elsif ($org eq 'yeast' && $featname eq 'gene' && $val =~ /SGD:/) { $id1= $val; } 
# 	  		elsif (!$id && $featname eq 'CDS' && $val =~ /PID:/) { $id1= $val; }
# 	  		 ## for yeast, need to move $id from CDS to gene (which hasnt a db_xref in ncbi genomes)
	  		if ($id1) { $id= $id1; }
				# else  ##? leave out if $id
				{ push(@dbx, $val); }
				}
  		
  		}
  	elsif ( m|^\s+([^"]+)|) { ## " continuation line
			if ($inrange) { $srange .= $1; chomp($srange); }
  		}
  	else { ## nothing else?
  		}
  	}
  return ($featname,$srange,$gsym,$map,$id,\@dbx,\%fnotes);
}


sub printFeat {
	my ($fh,$org,$seqid,@feat)= @_;

	my $srec= $clones{$seqid};
	my ($ctgid,$bpstart,$bplen)= split(/\t/,$srec);
	my $ctrec= $contigs{$ctgid};
	my ($csome,$cbpstart,$cbplen)= split(/\t/,$ctrec);
	#? save $seqid, $ctgid for each record?
	
	my ($featname,$srange,$gsym,$map,$id,$rdbx,$rfnotes)= parseFeat(@feat);
	
	# offset $map by $bpstart/$cbpstart !??
	# write to $fh->csome ?
	
# 	## 
# 	## need special fixes for genome/fly/scaffolds to weave into csome ordered data
# 	## & join w/ more updated flybase data
# 	## 
# 	my $isscaf= 0;
# 	if ($scaf) { ##  && $org eq 'fly'
# 		my $arange= scaffold2arm($scaf,$srange);
# 		## print STDERR "$srange => $arange\n" if $debug;
# 		$srange= $arange;
# 		if ($featname eq 'source') { 
# 			##! and need to build new 'source' from scaffolds
# 			$featname= 'scaffold'; 
# 			$gsym= $scaf->{name};
# 			$isscaf= 1;  
# 			}
# 		}
# 	if ($org eq 'fly') {
# 		if ($chromosome && $cytomap ne $chromosome) {
# 			readFlyCytomap($chromosome);
# 			$cytomap= $chromosome;
# 			}
# 		my $fbid;
# 		if ($id =~ /(FBgn\d+)/) { $fbid= $1; }
# 		else { foreach (@{$rdbx}) { $fbid= $1 if (/(FBgn\d+)/); } }
# 		if ($fbid) {
# 			my $cmap= flyfeatures::getCytomap($fbid); $map= $cmap if ($cmap);  
# 			my $fsym= flyfeatures::getSym($fbid); $gsym= $fsym if ($fsym);  
# 			}
# 		}
			
	unless($gsym) {
		if ($featname =~ /^source/) { $gsym= $org; }
		else { $gsym= '-'; }
		}
	unless($map) {
		if ($featname =~ /^(source|scaffold)/ && $csomeFile) { $map= $csomeFile; }
		else { $map= '-'; }
		}
	unless ($id) {
		$id= flybase::sym2id::symbol2id($gsym); ## $sym2id{ symcase($gsym) }; 
		}
	my $idsym= flybase::sym2id::id2symbol($id);
	$gsym= $idsym if($idsym); # make sure is proper symbol
	
	$allfeats{$featname}++;
	print $fh "$featname\t$gsym\t$map\t$srange\t$id\t";
	foreach (sort @{$rdbx}) { print $fh "$_,";}  
	
	if ($wantnotes) {
	print $fh "\t";
	foreach (sort keys %{$rfnotes}) { 
		print $fh "$_,";
		$allnotes{$_} += ${$rfnotes}{$_};
		}
	}
	print $fh "\tCHR_$csome:$seqid";
	print $fh "\n";
}


sub symcase {
	my($sym)= shift;
	## return uc($sym); ## if genbank doesnt keep proper case!
	return $sym;
}

#------> Fpc_Contig.txt.table.gz <------ >> 1396 lines
#cID    contigName        bpstart          bplen     csome
#871     ctg13815        25854336        2186457 18
sub readcontigs {
	my $fn= shift || ($mapdir . 'Fpc_Contig.txt.table.gz');
	my $ok;
	local(*D,*FH);
	%contigs= ();
	print STDERR "readcontigs($fn)\n" if $debug;
	if ($fn =~ /\.gz/) { $ok= open(FH,"gzcat $fn|"); } else { $ok= open(FH,$fn); }
	while (<FH>) {
	  chomp();
		my ($ctgid,$ctgname,$bpstart,$bplen,$csome) = split(); # /\t/ ?
		$contigs{$ctgid}= "$csome\t$bpstart\t$bplen";
		}
	close(FH);
}


#------> Fpc_Clone.txt.table.gz <------ >> 32253 lines
# Embl/Gb ID		Clone name      Orgzn. ContigID band  fpcSize  seqSize  seqStart?
#AP001105        RP11-759D19     JAPAN   871     0       0       164321  0
sub readclones {
	my $fn= shift || ($mapdir . 'Fpc_Clone.txt.table.gz');
	my $ok;
	local(*D,*FH);
	print STDERR "readclones($fn)\n" if $debug;
	%clones= ();
	if ($fn =~ /\.gz/) { $ok= open(FH,"gzcat $fn|"); } else { $ok= open(FH,$fn); }
	while (<FH>) {
	  chomp();
		my ($seqid,$cname,$og,$ctgid,$bd,$fsz,$bplen,$bpstart) = split();
		$clones{$seqid}= "$ctgid\t$bpstart\t$bplen";
		}
	close(FH);
}

__END__

ensembl maps/
CHECKSUMS.gz                   MarkChr.txt.table.gz
ChromosomeBands.txt.table.gz   Marker.txt.table.gz
CytogeneticMap.txt.table.gz    MarkerSynonym.txt.table.gz
Fpc_Clone.txt.table.gz         RHMaps.txt.table.gz
Fpc_Contig.txt.table.gz        help.txt.table.gz
LandmarkMarker.txt.table.gz    maps075.sql.gz
Map.txt.table.gz

build features/csome from ensembl:
#Feature        gene    cmap     bprange   id      db_xref notes

contigs(ctgid,rec)= readcontigs(ctgid, Fpc_Contig(ctgid,bpstart,bplen, csome))
clones(seqid,rec)= readclones(seqid, Fpc_Clone(seqid, seqsize, seqstart))
readensgb - foreach locus(seqid)
   foreach feature
      featkind, featname, cmap?,  bpmap,  egID,  dbxref, notes
      featname = ? from egID->sym map || from /gene="ENSG00000089311"
      egID = ? from /dbxref=LOCUSLINK  
  				also have REFSEQ,EMBL,SPTREMBL,HUGO,MIM,
  		bpmap = reformat of location -> 
  			flip?? 	join(complement(102579..102620),complement(102434..102574),...)
  			 to  complement(...,join(c..d),join(a..b))
  			add csome offset: 
  				ctgid= clones(seqid).ctgid
  				clones(seqid).start,len should == feat.location.start,len
  			  + contigs(ctgid).start,len
  			  
  	  cmap? == CytogeneticMap


build dna/csome from ensembl:
read2hash(ctgid, Fpc_Contig(ctgid,bpstart,bplen, csome))
read2hash(seqid, Fpc_Clone(seqid, seqsize, seqstart))
------> ens075.dna.fa.gz <------ >> these are seqid's
>AB000381.00001
GCGGCCGGAATTAACCCTCACTAAAGGGATCCCTCGATCATACACTATGTGGCCTCTGTGTCTGGCTTCTGT
>AB000381.00001
>AB012723.00001
>AB015355.00001
..
>AB020858.00001
>AB020859.00001
>AB020860.00001
>AB020861.00001
>AB020862.00001
...
>AC000003.00001
>AC000004.00001
>AC000007.00001
>AC000015.00001
>AC000021.00001
>AC000022.00001
>L47234.00001

  	 		 
------> Fpc_Contig.txt.table.gz <------ >> 1396 lines
#cID    contigName        bpstart          bplen     csome
871     ctg13815        25854336        2186457 18
1125    ctg15274        141041432       339582  X
652     ctg13492        72819205        3551438 12
943     ctg17057        54560273        214790  19
685     ctg16166        23449087        4607383 14
566     ctg13655        30582683        17914764        10
184     ctg14708        254158329       172797  2
125     ctg14546        7906646 2065334 2
986     ctg16167        -1      183481  21
491     ctg15438        0       952452  8

------> Fpc_Clone.txt.table.gz <------ >> 32253 lines
# Embl/Gb ID		Clone name      Orgzn. ContigID band  fpcSize  seqSize  seqStart?
AP001105        RP11-759D19     JAPAN   871     0       0       164321  0
AC015933        CTD-2023G8      WIBR    871     0       0       228390  12000
AP001145        RP11-687D24     JAPAN   871     0       0       183937  96000
AP001900        RP11-705A9      RIKEN   871     0       0       145550  112000


------> CytogeneticMap.txt.table.gz <------
RH2337  p36     p36     3       2       1       0
RH2124  p36     p36     1       1       1       0
RH31559 p36     p35     1               1       0

------> ChromosomeBands.txt.table.gz <------
1       1       w       p36     3       7800.63
1       2       b       p36     2       3719.51
1       3       w       p36     1       10590.26

------> LandmarkMarker.txt.table.gz <------
105129  D12S1957
106654  D4S3169
106926  D6S1886


------> MarkChr.txt.table.gz <------
RH1     17
RH2     10
RH3     1

------> Marker.txt.table.gz <------
RH1     CTGGTGAGGAAGCTCCAGTC    AACCCGATTAGCAAGGCC      cdna
RH2     GTGCTGGCCCTCATAGTGTT    AGGTTACAGCTGCTCCTGGA    cdna
RH3     AGGTAGCTCCCAGCACTCAA    TTTATTGGCTGGAAAGGGC
RH4     GCCTCCTCCTACTGTTTCCC    GAGGTCAGGCTTTAGCGATG    cdna

------> MarkerSynonym.txt.table.gz <------
RH1     RH1     RHdb
RH1     stSG1   Sanger_STS
RH1     SC91    RHalloc

------> RHMaps.txt.table.gz <------
GB4     RH50853 0.00    1
GB4     RH104552        0.58    1
GB4     RH75913 0.58    1

------> help.txt.table.gz <------
NotMapped       RH3     1
NotMapped       RH10    22

------> maps075.sql.gz <------
# MySQL dump 8.10
#
# Host: localhost    Database: maps075
#--------------------------------------------------------
# Server version        3.23.25-beta

#
# Table structure for table 'ChromosomeBands'
#

CREATE TABLE ChromosomeBands (
  chromosome char(2) DEFAULT 'un' NOT NULL,
  tag int(11) DEFAULT '0' NOT NULL,
  colour char(2),
  major_band char(3),
  minor_band char(10),
  length float(10,2),
  PRIMARY KEY (chromosome,tag)
);

#
# Table structure for table 'CytogeneticMap'
#

CREATE TABLE CytogeneticMap (
  marker varchar(40) DEFAULT '' NOT NULL,
  start_band varchar(40) DEFAULT '' NOT NULL,
  end_band varchar(40),
  start_sub_band varchar(40),
  end_sub_band varchar(40),
  chromosome varchar(10) DEFAULT '' NOT NULL,
  position_tag int(11) DEFAULT '0' NOT NULL,
  PRIMARY KEY (marker),
  KEY BandIdx (start_band),
  KEY ChromosomeIdx (chromosome),
  KEY posIdx (position_tag)
);

#
# Table structure for table 'Fpc_Clone'
#

CREATE TABLE Fpc_Clone (
  embl_id varchar(15) DEFAULT '' NOT NULL,
  clone_name varchar(20) DEFAULT '' NOT NULL,
  organisation varchar(15) DEFAULT '' NOT NULL,
  contig_id int(11) DEFAULT '0' NOT NULL,
  band int(11) DEFAULT '0' NOT NULL,
  fpc_size int(11) DEFAULT '0' NOT NULL,
  seq_size int(11),
  start_guess int(11),
  KEY contigIdx (contig_id),
  PRIMARY KEY (clone_name,embl_id),
  KEY embl_id (embl_id)
);

#
# Table structure for table 'Fpc_Contig'
#

CREATE TABLE Fpc_Contig (
  contig_id int(11) NOT NULL auto_increment,
  contig_name varchar(15) DEFAULT '' NOT NULL,
  start int(11) DEFAULT '0' NOT NULL,
  length int(11) DEFAULT '0' NOT NULL,
  chromosome char(3) DEFAULT '' NOT NULL,
  PRIMARY KEY (contig_id),
  KEY beginIdx (chromosome,start),
  KEY NameIdx (contig_name)
);

#
# Table structure for table 'LandmarkMarker'
#

CREATE TABLE LandmarkMarker (
  marker varchar(40) DEFAULT '' NOT NULL,
  name varchar(40) DEFAULT '' NOT NULL,
  KEY synname (name),
  PRIMARY KEY (marker,name)
);

#
# Table structure for table 'Map'
#

CREATE TABLE Map (
  id varchar(40) DEFAULT '' NOT NULL,
  name varchar(40),
  tablename varchar(40),
  origin varchar(40),
  version int(11),
  last_updated timestamp(14),
  PRIMARY KEY (id)
);

#
# Table structure for table 'MarkChr'
#

CREATE TABLE MarkChr (
  marker varchar(40) DEFAULT '' NOT NULL,
  chr varchar(5),
  PRIMARY KEY (marker)
);

#
# Table structure for table 'Marker'
#

CREATE TABLE Marker (
  marker varchar(40) DEFAULT '' NOT NULL,
  seq_left varchar(40) DEFAULT '' NOT NULL,
  seq_right varchar(40) DEFAULT '' NOT NULL,
  marker_type varchar(5) DEFAULT '' NOT NULL,
  PRIMARY KEY (marker),
  KEY leftIdx (seq_left),
  KEY rightIdx (seq_right)
);

#
# Table structure for table 'MarkerSynonym'
#

CREATE TABLE MarkerSynonym (
  marker varchar(40) DEFAULT '' NOT NULL,
  name varchar(40) DEFAULT '' NOT NULL,
  db varchar(15) DEFAULT '' NOT NULL,
  KEY synname (name),
  PRIMARY KEY (marker,name,db)
);

#
# Table structure for table 'RHMaps'
#

CREATE TABLE RHMaps (
  map varchar(40) DEFAULT '' NOT NULL,
  marker varchar(40) DEFAULT '' NOT NULL,
  map_position float(10,2) DEFAULT '-1.00' NOT NULL,
  chromosome varchar(10) DEFAULT '' NOT NULL,
  PRIMARY KEY (marker,map),
  KEY chrIdx (chromosome)
);

#
# Table structure for table 'help'
#

CREATE TABLE help (
  map varchar(40),
  marker varchar(40),
  chromosome varchar(10)
);
#----------------------

while(<DATA>) {
 if (/^component/) {
 	@v= split();
 	$l= $v[5] - $v[4];
 	print $_;
 	print "length= $l\n";
 	}
}

__DATA__
>> genbank length= 157089

Ensembl LOCUS feature IDs are in Fpc_Clone.txt.table == embl_id
and in genbank genome maps as 'component'

/c7/eugenes/human/ensembl/maps
oat% gzgrep -e 'AB019441|AC026279|AB019440' *gz
Fpc_Clone.txt.table.gz:AC026279 RP11-321G12     WUGSC   718     0       0 157159  1392000
Fpc_Clone.txt.table.gz:AB019441         JAPAN   702     0       0       157090 0
Fpc_Clone.txt.table.gz:AB019440         KYOTO   702     0       0       200000  200000

/c7/eugenes/human/ncbi/genomes/maps/chromosome_order
oat%  gzgrep -e 'AB019441|AC026279|AB019440' *gz
chr14_sequence.gz:component     4512311 AB019441.1      14      104253954 104411043       -
chr14_sequence.gz:component     4512300 AB019440.1      14      104461044 104661043       +
chr15_sequence.gz:component     8954310 AC026279.4      15      66275784 66432873        -
 
# loclink gene count = 19256
# grep -c 'RSQ|REFSEQ' acode  = 10786
# grep -c 'RPA|REFPROT' acode = 10799
#
# Ens_gene=44835 << many predicted
# Ens_LOCUSLINK=7844
# Ens_REFSEQ=17442
#
# NCBI_gene=8889

Ensembl gene annots. have
# LOCUSLINK=7844
# REFSEQ=17442 ?? many dups?

NCBI genomes has features:
 variation == /db_xref="dbSNP:689125" 
 STS /db_xref="UniSTS:184132" 
hs_chr11.gbs:
CDS     574
LOCUS   297
STS     6200
gene    545
mRNA    574
misc_feature    307
source  1891
variation       102980
 
 

LOCUS       AB019440   ENSEMBL; DNA; HTG; 200001 BP.     15-MAY-1999
     source          1..200001   
LOCUS       AB019441   ENSEMBL; DNA; HTG; 157091 BP.     15-MAY-1999

AC060783
    source          1..153156
    
AC026279
LOCUS       AC026279   ENSEMBL; DNA; HTG; 157160 BP.     24-AUG-2000

     source          1..157160
     CDS             join(complement(5466..5550),complement(46721..46900),
                     complement(45668..45810),AC023591:432..527,
                     AC023591:1746..1809,AC023591:2084..2241,28540..28666,
                     39355..39387,40252..40336,41128..41197)
                     /db_xref="EMBL:AF037335"
                     /db_xref="EMBL:AF051882"
                     /db_xref="HUGO:CA12"
                     /db_xref="LOCUSLINK:771"
                     /db_xref="MIM:603263"
                     /db_xref="REFSEQ:NP_001209"
                     /db_xref="SPTREMBL:O43570"
                     /transcript="ENST00000178638"
                     /cds="ENSP00000178638"
                     /gene="ENSG00000074410"

NCBI genomes maps chr15_sequence.gz:
component     8954310 AC026279.4      15      66275784 66432873        -

LOCUS       AB019441   ENSEMBL; DNA; HTG; 157091 BP.     15-MAY-1999
DEFINITION  Reannotated sequence via Ensembl
ACCESSION   AB019441
VERSION     AB019441.1
KEYWORDS    HTG; HTGS_PHASE.
SOURCE      Homo sapiens.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Vertebrata; Mammalia; Eutheria;
            Primates; Catarrhini; Hominidae; Homo.
COMMENT     This sequence was reannotated via the Ensembl system. Please visit
            the Ensembl web site, http://www.ensembl.org/ for more information.
COMMENT     The reference, comment, description and feature table of the
            original entry can be found in the DDBJ/EMBL/GenBank database with
            the identical accession number.
COMMENT     The /gene indicates a unique id for a gene, /cds a unique id for a
            translation and a /exon a unique id for an exon. These ids are
            maintained wherever possible between versions. For more information
            on how to interpret the feature table, please visit
            http://www.ensembl.org/Docs/embl.html.
COMMENT     All the exons and transcripts in Ensembl are confirmed by
            similarity to either protein or cDNA sequences.
COMMENT     In unfinished, rough draft DNA sequence gene structures can cross
            fragments and, in these cases, the order and orientation of the
            fragments is likely to be different from the order in the the
            International Nucleotide Sequence Databases DDBJ/EMBL/GenBank.
FEATURES             Location/Qualifiers
     source          1..157091
                     /organism="Homo sapiens"
     CDS             join(16680..16736)
                     /transcript="ENST00000203141"
                     /cds="ENSP00000203141"
                     /gene="ENSG00000089318"
                     /translation="TVCVCVCVCVCVCVCVCPL"
     CDS             join(17860..17905,36566..36870)
                     /db_xref="EMBL:X07448"
                     /db_xref="SPTREMBL:P23083"
                     /transcript="ENST00000004493"
                     /cds="ENSP00000004493"
                     /gene="ENSG00000003981"
                     /translation="MDWTWRILFLVAAATGAHSQVQLVQSGAEVKKPGASVKVSCKASG
                     YTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSR
                     LRSDDTAVYYCAR"
     CDS             join(55380..55427)
                     /transcript="ENST00000203134"
                     /cds="ENSP00000203134"
                     /gene="ENSG00000089311"
                     /translation="APVVLTCPPVCPNHSQ"
     CDS             join(79678..79770)
                     /transcript="ENST00000203129"
                     /cds="ENSP00000203129"
                     /gene="ENSG00000089306"
                     /translation="QWLTPVIPALWEAEAGGSLEVRTLRPAWPTW"
     CDS             join(95775..95831)
                     /transcript="ENST00000203127"
                     /cds="ENSP00000203127"
                     /gene="ENSG00000089304"
                     /translation="PREQTLRPGPEDGGGAESS"
     CDS             join(complement(102579..102620),complement(102434..102574),
                     complement(101459..101479),complement(101422..101454),
                     complement(101338..101419),complement(101038..101141))
                     /db_xref="EMBL:AF161538"
                     /db_xref="REFSEQ:NP_054870"
                     /db_xref="SPTREMBL:Q9NZY2"
                     /transcript="ENST00000203137"
                     /cds="ENSP00000203137"
                     /gene="ENSG00000089314"
                     /translation="EPGDTGPILPNGDTGAALRSRERPSWPQETHGHRERTEEGCAVAA
                     FSADALRTGGQELEQTGLRPKAGPLCQTSWVTGYTDIGKGWRMDGGRTCSCSSFCRCPE
                     RGARRSSPDAPGLALDFPLLLDLLWHLCSWTSQPLEL"
     CDS             join(complement(109919..109993))
                     /transcript="ENST00000203126"
                     /cds="ENSP00000203126"
                     /gene="ENSG00000089303"
                     /translation="SLSLPVGGDSSVGFPGEVWKGAGLR"
     exon            16680..16736
                     /start_phase=0
                     /exon_id="ENSE00000567233"
                     /end_phase=0
     exon            17860..17905
                     /start_phase=0
                     /exon_id="ENSE00000567229"
                     /end_phase=1
     exon            36566..36870
                     /start_phase=1
                     /exon_id="ENSE00000372030"
                     /end_phase=0
..
     repeat_region   complement(380..773)
                     /note="LTR52: matches 4 to 404 of consensus"
     repeat_region   1054..2080
                     /note="LTR5: matches 3 to 968 of consensus"
     repeat_region   complement(2140..3003)
                     /note="MER49: matches 3 to 916 of consensus"