first attempt at new parsers for zebrafish

misc-scripts/xref_mapping/XrefParser/ZFINDescParser.pm

+package XrefParser::ZFINDescParser;
+
+use strict;
+use POSIX qw(strftime);
+use File::Basename;
+use File::Spec::Functions;
+
+use base qw( XrefParser::BaseParser );
+
+# --------------------------------------------------------------------------------
+# Parse command line and run if being run directly
+
+if (!defined(caller())) {
+
+  if (scalar(@ARGV) != 1) {
+    print STDERR "\nUsage: ZFINDescParser.pm file <source_id> <species_id>\n\n";
+    exit(1);
+  }
+
+  run($ARGV[0]);
+
+}
+
+
+sub run {
+
+  my $self = shift if (defined(caller(1)));
+
+  my $source_id = shift;
+  my $species_id = shift;
+  my $files       = shift;
+  my $release_file   = shift;
+  my $verbose       = shift;
+
+  my $file = @{$files}[0];
+
+  if(!defined($source_id)){
+    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
+  }
+  if(!defined($species_id)){
+    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
+  }
+
+
+  open(FH,"<$file") || die "could not open file $file";
+  
+
+#e.g.
+#ZDB-GENE-000112-30      couptf2 long_desc
+
+  my $count =0;
+  while ( <FH> ) {
+    chomp;
+    my ($zfin, $label, $desc) = split (/\t/,$_);
+
+    $self->add_xref($zfin,"",$label,$desc,$source_id,$species_id,"MISC");
+    $count++;
+  }
+
+  if($verbose){
+    print "\t$count xrefs added\n";
+  }
+  return 0;
+}
+
+1;

misc-scripts/xref_mapping/XrefParser/ZFIN_DARTParser.pm

+package XrefParser::ZFIN_DARTParser;
+
+use strict;
+
+use DBI;
+
+use Bio::EnsEMBL::Registry;
+use base qw( XrefParser::BaseParser );
+my $reg = "Bio::EnsEMBL::Registry";
+
+# Parse file of HGNC records and assign direct xrefs
+# All assumed to be linked to genes
+
+
+
+sub run_script {
+
+  my $self = shift if (defined(caller(1)));
+
+  my $file = shift;
+  my $source_id = shift;
+  my $species_id = shift;
+  my $verbose = shift;
+
+  my ($type, $my_args) = split(/:/,$file);
+
+  my $host = "ens-staging1";
+  my $user = "ensro";
+
+  if($my_args =~ /host[=][>](\S+?)[,]/){
+    $host = $1;
+  }
+  if($my_args =~ /user[=][>](\S+?)[,]/){
+    $user = $1;
+  }
+
+  my $vuser;
+  my $vhost;
+  my $vport;
+  my $vdbname;
+  my $vpass;
+
+  if($my_args =~ /vhost[=][>](\S+?)[,]/){
+    $vhost = $1;
+  }
+  if($my_args =~ /vuser[=][>](\S+?)[,]/){
+    $vuser = $1;
+  }
+  if($my_args =~ /vport[=][>](\S+?)[,]/){
+    $vport =  $1;
+  }
+  if($my_args =~ /vdbname[=][>](\S+?)[,]/){
+    $vdbname = $1;
+  }
+  else{
+    print "No vdbname??? $my_args??\n";
+  }	
+  if($my_args =~ /vpass[=][>](\S+?)[,]/){
+    $vpass = $1;
+  }
+
+  my $cuser;
+  my $chost;
+  my $cport;
+  my $cdbname;
+  my $cpass;
+
+  if($my_args =~ /chost[=][>](\S+?)[,]/){
+    $chost = $1;
+  }
+  if($my_args =~ /cuser[=][>](\S+?)[,]/){
+    $cuser = $1;
+  }
+  if($my_args =~ /cport[=][>](\S+?)[,]/){
+    $cport =  $1;
+  }
+  if($my_args =~ /cdbname[=][>](\S+?)[,]/){
+    $cdbname = $1;
+  }
+  if($my_args =~ /cpass[=][>](\S+?)[,]/){
+    $cpass = $1;
+  }
+  my $vega_dbc;
+  my $core_dbc;
+  if(defined($vdbname)){
+    print "Using $host $vdbname for Vega and $cdbname for Core\n";
+    $vega_dbc = $self->dbi2($vhost, $vport, $vuser, $vdbname, $vpass);
+    if(!defined($vega_dbc)){
+      print "Problem could not open connectipn to $vhost, $vport, $vuser, $vdbname, $vpass\n";
+      return 1;
+    }
+    $core_dbc = $self->dbi2($chost, $cport, $cuser, $cdbname, $cpass);
+    if(!defined($core_dbc)){
+      print "Problem could not open connectipn to $chost, $cport, $cuser, $cdbname, $cpass\n";
+      return 1;
+    }
+
+  }
+  else{
+    $reg->load_registry_from_db(
+                                -host => $host,
+                                -user => $user);
+
+    $vega_dbc = $reg->get_adaptor("zebrafish","vega","slice");
+    if(!defined($vega_dbc)){
+      print "Could not connect to human vega database using load_registry_from_db $host $user\n";
+      return 1;
+    }
+    $vega_dbc = $vega_dbc->dbc;
+    $core_dbc = $reg->get_adaptor("zebrafish","core","slice");
+    if(!defined($core_dbc)){
+      print "Could not connect to danio_rerio core database using load_registry_from_db $host $user\n";
+      return 1;
+    }
+    $core_dbc= $core_dbc->dbc;
+  }
+
+
+
+  $source_id = XrefParser::BaseParser->get_source_id_for_source_name("ZFIN_ID","vega");
+
+
+  my $sql = 'select tsi.stable_id, x.display_label from xref x, object_xref ox , transcript_stable_id tsi, external_db e where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and e.db_name like ?';
+
+
+  my $hgnc_sql = 'select tsi.stable_id, x.dbprimary_acc from xref x, object_xref ox , transcript_stable_id tsi, gene g, external_db e, transcript t  where t.gene_id = g.gene_id and g.gene_id = ox.ensembl_id and tsi.transcript_id = t.transcript_id and e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and ox.ensembl_object_type = "Gene" and e.db_name like "ZFIN_ID"';
+
+
+  my %ott_to_hgnc;
+  my %ott_to_enst;
+
+  my $sth = $core_dbc->prepare($sql) || die "Could not prepare for core $sql\n";
+
+  foreach my $external_db (qw(OTTT shares_CDS_and_UTR_with_OTTT shares_CDS_with_OTTT)){
+    $sth->execute($external_db) or croak( $core_dbc->errstr());
+    while ( my @row = $sth->fetchrow_array() ) {
+      $ott_to_enst{$row[1]} = $row[0];
+    }
+  }
+
+  print "We have ".scalar(%ott_to_enst)." ott to enst entries\n " if($verbose);
+
+  $sth = $vega_dbc->prepare($hgnc_sql) || die "could not prepare vega sql: $hgnc_sql";
+  $sth->execute() or croak( $vega_dbc->errstr() );
+
+  while ( my @row = $sth->fetchrow_array() ) {
+    $ott_to_hgnc{$row[0]} = $row[1];
+  }
+  $sth->finish;
+  print "We have ".scalar(%ott_to_hgnc)." ott to zfin entries\n" if($verbose);
+
+
+  my $line_count = 0;
+  my $xref_count = 0;
+
+  # becouse the direct mapping have no descriptions etc
+  # we have to steal these fromt he previous HGNC parser.
+  # This is why the order states this is after the other one.
+  # maybe 1091,1092 is not right maybe should use name = HGNC and priority = 30r4 ??
+
+  my %label;
+  my %version;
+  my %description;
+
+  my $dbi = $self->dbi();  
+
+
+  my $sql = "insert into synonym (xref_id, synonym) values (?, ?)";
+  my $add_syn_sth = $dbi->prepare($sql);    
+  
+  my $syn_hash = $self->get_zfin_synonyms();
+  
+
+
+  #get the source ids for HGNC refseq, entrezgene and unitprot
+  $sql = 'select source_id, priority_description from source where name like "ZFIN_ID"';
+  $sth = $dbi->prepare($sql);
+  
+  $sth->execute();
+
+
+  my ($hgnc_source_id, $desc);
+  $sth->bind_columns(\$hgnc_source_id, \$desc);
+  my @arr;
+  while($sth->fetch()){
+    push @arr, $hgnc_source_id;
+  }
+  $sth->finish;
+  
+  $sql = "select accession, label, version,  description from xref where source_id in (".join(", ",@arr).")";
+#  print "$sql\n";;
+  $sth = $dbi->prepare($sql);
+  $sth->execute();
+  my ($acc, $lab, $ver);
+  my $hgnc_loaded_count = 0;
+  $sth->bind_columns(\$acc, \$lab, \$ver, \$desc);
+  while (my @row = $sth->fetchrow_array()) {
+    $label{$acc} = $lab;
+    $version{$acc} = $ver;
+    $description{$acc} = $desc;
+    $hgnc_loaded_count++;
+  }
+  $sth->finish;
+  if($hgnc_loaded_count == 0){
+    die "No point continuing no hgncs there\n";
+  }
+
+
+  my $ignore_count = 0;
+  my $ignore_examples ="";
+  my %acc;
+
+  foreach my $key ( keys %ott_to_hgnc){
+    if(defined($ott_to_enst{$key} )){
+      
+      my $hgnc = $ott_to_hgnc{$key};
+      $hgnc =~ s/ZFIN_ID://;
+      my $stable_id = $ott_to_enst{$key};
+
+      if(!defined($label{$hgnc})){
+	$ignore_count++;
+	if($ignore_count < 10){
+	  $ignore_examples .= " ".$hgnc;
+	}
+	next;
+      }
+      if(!defined($acc{$hgnc})){
+	$acc{$hgnc} = 1;
+	my $version ="";
+	$line_count++;
+	
+	my $xref_id = $self->add_xref($hgnc, $version{$hgnc} , $label{$hgnc}||$hgnc , $description{$hgnc}, $source_id, $species_id, "DIRECT");
+	$xref_count++;
+	
+	
+	$self->add_direct_xref($xref_id, $stable_id, "transcript", "");
+
+	if(defined($syn_hash->{$hgnc})){
+	  foreach my $syn (@{$syn_hash->{$hgnc}}){
+	    $add_syn_sth->execute($xref_id, $syn);
+	  }
+	}
+
+      }
+    }
+  }
+  $add_syn_sth->finish;
+  print "Parsed $line_count ZFIN identifiers from $file, added $xref_count xrefs and $line_count direct_xrefs\n" if($verbose);
+  if($ignore_count){
+    print $ignore_count." ignoreed due to numbers no identifiers being no longer valid :- $ignore_examples\n" if($verbose);
+  }
+  
+  
+  return 0;
+}
+
+
+sub get_zfin_synonyms{
+  my $self = shift;
+  my %hgnc_syns;
+  my %seen;          # can be in more than once fro each type of hgnc.
+
+  my $sql = (<<SYN);
+SELECT  x.accession, x.label, sy.synonym 
+  FROM xref x, source so, synonym sy
+    WHERE x.xref_id = sy.xref_id
+      AND so.source_id = x.source_id
+      AND so.name like "ZFIN_ID"
+SYN
+
+  my $dbi = $self->dbi();
+  my $sth = $dbi->prepare($sql);    
+
+  $sth->execute;
+  my ($acc, $label, $syn);
+  $sth->bind_columns(\$acc, \$label, \$syn);
+
+  my $count = 0;
+  while($sth->fetch){
+    if(!defined($seen{$acc.":".$syn})){
+      push @{$hgnc_syns{$acc}}, $syn;
+      push @{$hgnc_syns{$label}}, $syn;
+      $count++;
+    }
+    $seen{$acc.":".$syn} = 1;
+  }
+  $sth->finish;
+
+  return \%hgnc_syns;
+
+}
+
+1;