Commit 914275ae authored by Monika Komorowska's avatar Monika Komorowska
Browse files

Changes to UniProtDirectParser - it can be used by any species

parent 50fa6136
...@@ -6,6 +6,7 @@ use Carp; ...@@ -6,6 +6,7 @@ use Carp;
use DBI; use DBI;
use base qw( XrefParser::BaseParser ); use base qw( XrefParser::BaseParser );
use XrefParser::Database;
# Parse file of Uniprot records and assign direct xrefs # Parse file of Uniprot records and assign direct xrefs
# All assumed to be linked to translation # All assumed to be linked to translation
...@@ -13,30 +14,67 @@ use base qw( XrefParser::BaseParser ); ...@@ -13,30 +14,67 @@ use base qw( XrefParser::BaseParser );
# -------------------------------------------------------------------------------- # --------------------------------------------------------------------------------
sub run { sub run_script {
my ($self, $ref_arg) = @_; my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id}; my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id}; my $species_id = $ref_arg->{species_id};
my $files = $ref_arg->{files}; my $file = $ref_arg->{file};
my $verbose = $ref_arg->{verbose}; my $verbose = $ref_arg->{verbose};
if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){ if((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
croak "Need to pass source_id, species_id and files as pairs"; croak "Need to pass source_id, species_id and file as pairs";
} }
$verbose |=0; $verbose |=0;
my %prefix = (9606 => "ENSP0", 10090 => "ENSMUSP0", 10116 => "ENSRNOP0"); my $user = "ensro";
my $host;
my $port;
my $dbname;
my $wget = "";
if(!defined($prefix{$species_id})){ if($file =~ /host[=][>](\S+?)[,]/){
print "No prefix known for this species $species_id???\n"; $host = $1;
}
if($file =~ /port[=][>](\S+?)[,]/){
$port = $1;
}
if($file =~ /dbname[=][>](\S+?)[,]/){
$dbname = $1;
}
if($file =~ /wget[=][>](\S+?)[,]/){
$wget = $1;
}
my $ua = LWP::UserAgent->new();
$ua->timeout(10);
$ua->env_proxy();
my $response = $ua->get($wget);
if ( !$response->is_success() ) {
warn($response->status_line);
return 1;
}
my $production_db = XrefParser::Database->new({ host => $host,
port => $port,
user => $user,
dbname => $dbname,
pass => ""});
my $prod_dbi = $production_db->dbi();
if(!defined($prod_dbi)){
return 1; return 1;
} }
my $filename = @{$files}[0]; my ($prefix) = $prod_dbi->selectrow_array("SELECT species_prefix FROM species WHERE taxon = $species_id");
my $file_io = $self->get_filehandle($filename); my %prefix = ($species_id => $prefix);
if ( !defined($file_io) ) {
if(!defined($prefix{$species_id})){
print "No prefix known for this species $species_id???\n";
return 1; return 1;
} }
...@@ -46,7 +84,9 @@ sub run { ...@@ -46,7 +84,9 @@ sub run {
my %prot2ensembl; my %prot2ensembl;
my $count = 0; my $count = 0;
while ( defined( my $line = $file_io->getline() ) ) {
my @lines = split(/\n/,$response->content);
foreach my $line (@lines){
my ($prot, $ens) = split /\s+/,$line; my ($prot, $ens) = split /\s+/,$line;
if($ens =~ /$prefix{$species_id}/){ if($ens =~ /$prefix{$species_id}/){
push @{$prot2ensembl{$prot}}, $ens; push @{$prot2ensembl{$prot}}, $ens;
......
<
...@@ -2598,7 +2598,7 @@ data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/unipro ...@@ -2598,7 +2598,7 @@ data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/unipro
# swissprot entry # swissprot entry
[source Uniprot/SWISSPROT::DIRECT] [source Uniprot/SWISSPROT::DIRECT]
# Used by homo_sapiens
name = Uniprot/SWISSPROT name = Uniprot/SWISSPROT
download = Y download = Y
order = 22 order = 22
...@@ -2607,8 +2607,7 @@ prio_descr = uniprot_mapped ...@@ -2607,8 +2607,7 @@ prio_descr = uniprot_mapped
parser = UniProtDirectParser parser = UniProtDirectParser
dependent = Unprot/SWISSPROT dependent = Unprot/SWISSPROT
release_uri = release_uri =
data_uri = ftp://ftp.ebi.ac.uk/pub/contrib/xrefs/ens-sp.map data_uri = script:wget=>ftp://ftp.ebi.ac.uk/pub/contrib/xrefs/ens-sp.map,host=>ens-staging1,dbname=>ensembl_production,
[source Uniprot/SWISSPROT::MULTI-predicted] [source Uniprot/SWISSPROT::MULTI-predicted]
...@@ -3563,6 +3562,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian ...@@ -3563,6 +3562,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
[species anopheles_gambiae] [species anopheles_gambiae]
taxonomy_id = 7165 taxonomy_id = 7165
...@@ -3945,6 +3945,7 @@ source = RefSeq_peptide::bos_taurus ...@@ -3945,6 +3945,7 @@ source = RefSeq_peptide::bos_taurus
source = UniGene::bos_taurus source = UniGene::bos_taurus
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
source = goslim_goa::MULTI source = goslim_goa::MULTI
...@@ -3976,6 +3977,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian ...@@ -3976,6 +3977,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
[species canis_familiaris] [species canis_familiaris]
taxonomy_id = 9615 taxonomy_id = 9615
...@@ -3990,6 +3992,7 @@ source = RefSeq_peptide::canis_familiaris ...@@ -3990,6 +3992,7 @@ source = RefSeq_peptide::canis_familiaris
source = UniGene::canis_familiaris source = UniGene::canis_familiaris
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species ciona_intestinalis] [species ciona_intestinalis]
...@@ -4005,6 +4008,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other ...@@ -4005,6 +4008,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other
source = UniGene::ciona_intestinalis source = UniGene::ciona_intestinalis
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = cint_aniseed_v1::ciona_intestinalis source = cint_aniseed_v1::ciona_intestinalis
source = cint_aniseed_v2::ciona_intestinalis source = cint_aniseed_v2::ciona_intestinalis
source = cint_jgi_v1::ciona_intestinalis source = cint_jgi_v1::ciona_intestinalis
...@@ -4025,6 +4029,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other ...@@ -4025,6 +4029,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other
source = UniGene::ciona_savignyi source = UniGene::ciona_savignyi
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species culex_quinquefasciatus] [species culex_quinquefasciatus]
...@@ -4056,6 +4061,7 @@ source = RefSeq_peptide::danio_rerio ...@@ -4056,6 +4061,7 @@ source = RefSeq_peptide::danio_rerio
source = UniGene::danio_rerio source = UniGene::danio_rerio
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ZFIN_ID::danio_rerio#01 source = ZFIN_ID::danio_rerio#01
source = ZFIN_ID::danio_rerio#02 source = ZFIN_ID::danio_rerio#02
source = ZFIN_ID::danio_rerio#03 source = ZFIN_ID::danio_rerio#03
...@@ -4072,6 +4078,7 @@ source = InterproGO::MULTI ...@@ -4072,6 +4078,7 @@ source = InterproGO::MULTI
source = Interpro::MULTI source = Interpro::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species dictyostelium_discoideum] [species dictyostelium_discoideum]
...@@ -4328,6 +4335,7 @@ source = InterproGO::MULTI ...@@ -4328,6 +4335,7 @@ source = InterproGO::MULTI
source = Interpro::MULTI source = Interpro::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species erinaceus_europaeus] [species erinaceus_europaeus]
...@@ -4343,6 +4351,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian ...@@ -4343,6 +4351,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = UniGene::MULTI source = UniGene::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species equus_caballus] [species equus_caballus]
...@@ -4358,6 +4367,7 @@ source = RefSeq_peptide::equus_caballus ...@@ -4358,6 +4367,7 @@ source = RefSeq_peptide::equus_caballus
source = UniGene::equus_caballus source = UniGene::equus_caballus
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species felis_catus] [species felis_catus]
...@@ -4370,6 +4380,7 @@ source = InterproGO::MULTI ...@@ -4370,6 +4380,7 @@ source = InterproGO::MULTI
source = Interpro::MULTI source = Interpro::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species gallus_gallus] [species gallus_gallus]
...@@ -4386,6 +4397,7 @@ source = RefSeq_peptide::gallus_gallus ...@@ -4386,6 +4397,7 @@ source = RefSeq_peptide::gallus_gallus
source = UniGene::gallus_gallus source = UniGene::gallus_gallus
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species gasterosteus_aculeatus] [species gasterosteus_aculeatus]
...@@ -4401,6 +4413,7 @@ source = RefSeq_dna::gasterosteus_aculeatus ...@@ -4401,6 +4413,7 @@ source = RefSeq_dna::gasterosteus_aculeatus
source = RefSeq_peptide::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species gorilla_gorilla] [species gorilla_gorilla]
...@@ -4415,6 +4428,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian ...@@ -4415,6 +4428,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
...@@ -4470,6 +4484,7 @@ source = InterproGO::MULTI ...@@ -4470,6 +4484,7 @@ source = InterproGO::MULTI
source = Interpro::MULTI source = Interpro::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
...@@ -4486,6 +4501,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian ...@@ -4486,6 +4501,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = UniGene::macaca_mulatta source = UniGene::macaca_mulatta
source = ncRNA::MULTI source = ncRNA::MULTI
...@@ -4519,6 +4535,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian ...@@ -4519,6 +4535,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = UniGene::monodelphis_domestica source = UniGene::monodelphis_domestica
source = ncRNA::MULTI source = ncRNA::MULTI
...@@ -4565,6 +4582,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian ...@@ -4565,6 +4582,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = UniGene::myotis_lucifugus source = UniGene::myotis_lucifugus
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species ochotona_princeps] [species ochotona_princeps]
...@@ -4579,6 +4597,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian ...@@ -4579,6 +4597,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species ornithorhynchus_anatinus] [species ornithorhynchus_anatinus]
...@@ -4592,6 +4611,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian ...@@ -4592,6 +4611,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = Oxford_FGU_Oa_tscript::ornithorhynchus_anatinus source = Oxford_FGU_Oa_tscript::ornithorhynchus_anatinus
source = Oxford_FGU_Oa_gene::ornithorhynchus_anatinus source = Oxford_FGU_Oa_gene::ornithorhynchus_anatinus
source = Platypus_olfactory_receptor::ornithorhynchus_anatinus source = Platypus_olfactory_receptor::ornithorhynchus_anatinus
...@@ -4607,6 +4627,7 @@ source = InterproGO::MULTI ...@@ -4607,6 +4627,7 @@ source = InterproGO::MULTI
source = Interpro::MULTI source = Interpro::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species oryzias_latipes] [species oryzias_latipes]
...@@ -4622,6 +4643,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other ...@@ -4622,6 +4643,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other
source = UniGene::MULTI source = UniGene::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = UniProt::protein_id source = UniProt::protein_id
source = Uniprot::EMBL source = Uniprot::EMBL
source = ncRNA::MULTI source = ncRNA::MULTI
...@@ -4640,6 +4662,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian ...@@ -4640,6 +4662,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = UniGene::MULTI source = UniGene::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = Uniprot::EMBL source = Uniprot::EMBL
source = UniProt::protein_id source = UniProt::protein_id
...@@ -4669,6 +4692,7 @@ source = Interpro::MULTI ...@@ -4669,6 +4692,7 @@ source = Interpro::MULTI
source = UniGene::aedes_aegypti source = UniGene::aedes_aegypti
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
[species pongo_abelii] [species pongo_abelii]
taxonomy_id = 9601 taxonomy_id = 9601
...@@ -4683,6 +4707,7 @@ source = RefSeq_peptide::pongo_abelii ...@@ -4683,6 +4707,7 @@ source = RefSeq_peptide::pongo_abelii
source = UniGene::MULTI source = UniGene::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species procavia_capensis] [species procavia_capensis]
...@@ -4697,6 +4722,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian ...@@ -4697,6 +4722,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
...@@ -4712,6 +4738,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian ...@@ -4712,6 +4738,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species rattus_norvegicus] [species rattus_norvegicus]
...@@ -4747,7 +4774,7 @@ source = RefSeq_peptide::MULTI-fungi ...@@ -4747,7 +4774,7 @@ source = RefSeq_peptide::MULTI-fungi
source = SGD::saccharomyces_cerevisiae source = SGD::saccharomyces_cerevisiae
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
[species schizosaccharomyces_pombe] [species schizosaccharomyces_pombe]
taxonomy_id = 4896 taxonomy_id = 4896
...@@ -4778,6 +4805,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian ...@@ -4778,6 +4805,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = UniGene::MULTI source = UniGene::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = Uniprot::EMBL source = Uniprot::EMBL
source = UniProt::protein_id source = UniProt::protein_id
...@@ -4795,6 +4823,7 @@ source = RefSeq_dna::MULTI-complete ...@@ -4795,6 +4823,7 @@ source = RefSeq_dna::MULTI-complete
source = RefSeq_peptide::MULTI-complete source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::EG source = ncRNA::EG
source = misc_EG::EG source = misc_EG::EG
...@@ -4908,6 +4937,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian ...@@ -4908,6 +4937,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = UniGene::MULTI source = UniGene::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species taeniopygia_guttata] [species taeniopygia_guttata]
...@@ -4923,6 +4953,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other ...@@ -4923,6 +4953,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other
source = UniGene::taeniopygia_guttata source = UniGene::taeniopygia_guttata
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species takifugu_rubripes] [species takifugu_rubripes]
...@@ -4938,6 +4969,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other ...@@ -4938,6 +4969,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other
source = UniGene::takifugu_rubripes source = UniGene::takifugu_rubripes
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species tarsius_syrichta] [species tarsius_syrichta]
...@@ -4952,6 +4984,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian ...@@ -4952,6 +4984,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species tetraodon_nigroviridis] [species tetraodon_nigroviridis]
...@@ -4966,6 +4999,7 @@ source = RefSeq_dna::MULTI-vertebrate_other ...@@ -4966,6 +4999,7 @@ source = RefSeq_dna::MULTI-vertebrate_other
source = RefSeq_peptide::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
source = Genoscope_pred_gene::tetraodon_nigroviridis source = Genoscope_pred_gene::tetraodon_nigroviridis
source = Genoscope_pred_transcript::tetraodon_nigroviridis source = Genoscope_pred_transcript::tetraodon_nigroviridis
...@@ -4986,6 +5020,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian ...@@ -4986,6 +5020,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = UniGene::MULTI source = UniGene::MULTI
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species tursiops_truncatus] [species tursiops_truncatus]
...@@ -5000,6 +5035,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian ...@@ -5000,6 +5035,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::MULTI source = ncRNA::MULTI
[species vicugna_pacos] [species vicugna_pacos]