XrefParser::ZFINParser Class Reference
Public Member Functions | |
| public | run () |
Detailed Description
Definition at line 6 of file ZFINParser.pm.
Member Function Documentation
◆ run()
| public XrefParser::ZFINParser::run | ( | ) |
Undocumented method
Code:
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sub run {
my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $files = $ref_arg->{files};
my $verbose = $ref_arg->{verbose};
my $dbi = $ref_arg->{dbi};
$dbi = $self->dbi unless defined $dbi;
if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){
croak "Need to pass source_id, species_id and files as pairs";
}
$verbose |=0;
my $file = @{$files}[0];
my $dir = dirname($file);
# Get the ZFIN source ids
my $direct_src_id = $self->get_source_id_for_source_name('ZFIN_ID', 'direct', $dbi);
my $dependent_src_id = $self->get_source_id_for_source_name('ZFIN_ID', 'uniprot/refseq', $dbi);
my $description_src_id = $self->get_source_id_for_source_name('ZFIN_ID', 'description_only', $dbi);
# Get the ZFIN descriptions
my %description;
my $sth = $dbi->prepare("select accession, description from xref where source_id=?");
$sth->execute($description_src_id);
my ($acc, $desc);
my $zfin_loaded_count = 0;
$sth->bind_columns(\$acc, \$desc);
while (my @row = $sth->fetchrow_array()) {
$description{$acc} = $desc if(defined($desc));
$zfin_loaded_count++;
}
$sth->finish;
# Get the Uniprot and RefSeq accessions
my (%swiss) = %{$self->get_valid_codes("uniprot/swissprot",$species_id, $dbi)};
my (%refseq) = %{$self->get_valid_codes("refseq",$species_id, $dbi)};
# Process ZFIN to ensEMBL mappings
my %zfin;
my $zfin_io = $self->get_filehandle(catfile($dir, 'ensembl_1_to_1.txt'));
if (!defined($zfin_io)) {
croak "ERROR: Could not open " . catfile($dir, 'ensembl_1_to_1.txt') . "\n";
}
my $zfin_csv = Text::CSV->new({
sep_char => "\t",
empty_is_undef => 1,
strict => 1,
}) or croak "Could not use zfin file: " . Text::CSV->error_diag();
$zfin_csv->column_names(['zfin', 'so', 'label', 'ensembl_id']);
while (my $zfin_line = $zfin_csv->getline_hr($zfin_io)) {
my ($zfin_acc, $so, $label, $ensembl_id) = @{$zfin_line}{qw(zfin so label ensembl_id)};
$self->add_to_direct_xrefs({
stable_id => $ensembl_id,
type => 'gene',
acc => $zfin_acc,
label => $label,
desc => $description{$zfin_acc},
dbi => $dbi,
source_id => $direct_src_id,
species_id => $species_id
});
$zfin{$zfin_acc} = 1;
}
$zfin_io->close();
my $spcount =0;
my $rscount =0;
my $mismatch=0;
# Process ZFIN to Uniprot mappings
my $swissprot_io = $self->get_filehandle( catfile( $dir, 'uniprot.txt' ) );
if ( !defined $swissprot_io ) {
croak "ERROR: Could not open " . catfile( $dir, 'uniprot.txt' ). "\n" ;
}
my $swissprot_csv = Text::CSV->new({
sep_char => "\t",
empty_is_undef => 1,
strict => 1,
}) or croak "Could not use swissprot file $file: " . Text::CSV->error_diag();
$swissprot_csv->column_names([ 'zfin', 'so', 'label', 'acc' ]);
#swissprot file format (in uniprot.txt)
#ZDB-GENE-000112-47 SO:0000704 ppardb Q90Z66
#ZDB-GENE-000125-12 SO:0000704 igfbp2a Q9PTH3
#ZDB-GENE-000125-4 SO:0000704 dlc B3DFM3
while ( my $swissprot_line = $swissprot_csv->getline_hr( $swissprot_io ) ) {
my ($zfin_acc, $so, $label, $acc) = @{$swissprot_line}{qw(zfin so label acc)};
if(defined($swiss{$acc}) && !defined($zfin{$zfin_acc})){
foreach my $xref_id (@{$swiss{$acc}}){
$self->add_dependent_xref({
master_xref_id => $xref_id,
acc => $zfin_acc,
label => $label,
desc => $description{$zfin_acc},
source_id => $dependent_src_id,
dbi => $dbi,
species_id => $species_id
});
$spcount++;
}
} else {
$mismatch++;
}
}
$swissprot_io->close();
# Process ZFIN to RefSeq mappings
my $refseq_io = $self->get_filehandle( catfile( $dir, 'refseq.txt' ) );
if ( !defined $refseq_io ) {
croak "ERROR: Could not open " . catfile( $dir, 'refseq.txt' ),"\n" ;
}
my $refseq_csv = Text::CSV->new({
sep_char => "\t",
empty_is_undef => 1,
strict => 1,
}) or croak "could not use refseq file $file: " . Text::CSV->error_diag();
$refseq_csv->column_names([ 'zfin', 'so', 'label', 'acc' ]);
#ZDB-GENE-000125-12 SO:0000704 igfbp2a NP_571533
#ZDB-GENE-000125-4 SO:0000704 dlc NM_130944
#ZDB-GENE-000125-4 SO:0000704 dlc NP_571019
#ZDB-GENE-000128-11 SO:0000704 dbx1b NM_131178
while ( my $refseq_line = $refseq_csv->getline_hr( $refseq_io ) ) {
my ($zfin_acc, $so, $label, $acc) = @{$refseq_line}{qw(zfin so label acc)};
# Ignore mappings to predicted RefSeq
if ($acc =~ /^XP_/ || $acc =~ /^XM_/ || $acc =~ /^XR_/) { next; }
if(defined($refseq{$acc}) && !defined($zfin{$zfin_acc})){
foreach my $xref_id (@{$refseq{$acc}}){
$self->add_dependent_xref({
master_xref_id => $xref_id,
acc => $zfin_acc,
label => $label,
desc => $description{$zfin_acc},
source_id => $dependent_src_id,
dbi => $dbi,
species_id => $species_id
});
$rscount++;
}
} else {
$mismatch++;
}
}
$refseq_io->close();
# Get the added ZFINs again (with deps)
(%zfin) = %{$self->get_valid_codes("zfin", $species_id, $dbi)};
# Process the synonyms
my $aliases_io = $self->get_filehandle( catfile( $dir, 'aliases.txt' ) );
if ( !defined $aliases_io ) {
croak "ERROR: Could not open " . catfile( $dir, 'aliases.txt' ), "\n" ;
}
my $aliases_csv = Text::CSV->new({
sep_char => '\t',
empty_is_undef => 1,
strict => 1,
}) or croak "could not use zfin file $file: " . Text::CSV->error_diag();
$aliases_csv->column_names([ 'acc', 'cur_name', 'cur_symbol', 'syn', 'so' ]);
#DB-ALT-000717-2 zc1Tg zc1Tg zc1 SO:0001218
#ZDB-ALT-000717-4 zc3Tg zc3Tg Tg(NBT:MAPT-GFP) SO:0001218
my $syncount = 0;
$sth = $dbi->prepare('SELECT source_id from source where name like "ZFIN_ID"');
$sth->execute;
my $s1;
$sth->bind_columns(\$s1);
my $sources;
while($sth->fetch()){
push @$sources, $s1;
}
$sth->finish;
while ( my $aliases_line = $aliases_csv->getline_hr( $aliases_io ) ) {
my ($acc, $syn) = @{$aliases_line}{qw(acc syn)};
if(defined($zfin{$acc})){
$self->add_to_syn_for_mult_sources($acc, $sources, $syn, $species_id, $dbi);
$syncount++;
}
}
$aliases_io->close();
if($verbose){
print "\t$spcount xrefs from UniProt and\n";
print "\t$rscount xrefs from RefSeq succesfully loaded\n";
print "\t$syncount synonyms loaded\n";
print "\t$mismatch xrefs ignored\n";
}
return 0;
}
The documentation for this class was generated from the following file:
- ensembl/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
