XrefParser::RefSeqParser Class Reference
Public Member Functions | |
| public | run () |
| public | create_xrefs () |
Detailed Description
Definition at line 4 of file RefSeqParser.pm.
Member Function Documentation
◆ create_xrefs()
| public XrefParser::RefSeqParser::create_xrefs | ( | ) |
Undocumented method
Code:
click to view
sub create_xrefs {
my ($self, $peptide_source_id, $pred_peptide_source_id,
$mrna_source_id, $ncrna_source_id,
$pred_mrna_source_id, $pred_ncrna_source_id, $file, $species_id, $dbi ) = @_;
# Create a hash of all valid names for this species
my %species2name = $self->species_id2name($dbi);
my @names = @{$species2name{$species_id}};
my %name2species_id = map{ $_=>$species_id } @names;
# my %name2species_id = $self->name2species_id();
my $refseq_io = $self->get_filehandle($file);
if ( !defined $refseq_io ) {
print STDERR "ERROR: Can't open RefSeq file $file\n";
return;
}
my @xrefs;
local $/ = "\n>";
while ( $_ = $refseq_io->getline() ) {
my $xref;
my $entry = $_;
chomp $entry;
my ($header, $sequence) = split (/\n/, $entry, 2);
$sequence =~ s/^>//;
# remove newlines
my @seq_lines = split (/\n/, $sequence);
$sequence = join("", @seq_lines);
(my $acc, my $description) = split(/\s/, $header, 2);
$acc =~ s/^>//;
my ($species, $mrna);
if ($file =~ /\.faa(\.gz|\.Z)?$/) {
($mrna, $description, $species) = $description =~ /(\S*)\s+(.*)\s+\[(.*)\]$/;
$xref->{SEQUENCE_TYPE} = 'peptide';
$xref->{STATUS} = 'experimental';
my $source_id;
if ($acc =~ /^XP_/) {
$source_id = $pred_peptide_source_id;
} else {
$source_id = $peptide_source_id;
}
$xref->{SOURCE_ID} = $source_id;
} elsif ($file =~ /\.fna(\.gz|\.Z)?$/) {
($species, $description) = $description =~ /\s*(\w+\s+\w+)\s+(.*)$/;
$xref->{SEQUENCE_TYPE} = 'dna';
$xref->{STATUS} = 'experimental';
my $source_id;
if ($acc =~ /^XM_/ ){
$source_id = $pred_mrna_source_id;
} elsif( $acc =~ /^XR/) {
$source_id = $pred_ncrna_source_id;
} elsif( $acc =~ /^NM/) {
$source_id = $mrna_source_id;
} elsif( $acc =~ /^NR/) {
$source_id = $ncrna_source_id;
}
$xref->{SOURCE_ID} = $source_id;
}
if (!$species) { next; }
$species = lc $species;
$species =~ s/ /_/;
my $species_id_check = $name2species_id{$species};
# skip xrefs for species that aren't in the species table
if ( defined $species_id
&& defined $species_id_check
&& $species_id == $species_id_check )
{
my ($acc_no_ver,$ver) = split (/\./,$acc);
$xref->{ACCESSION} = $acc_no_ver;
$xref->{VERSION} = $ver;
$xref->{LABEL} = $acc;
$xref->{DESCRIPTION} = $description;
$xref->{SEQUENCE} = $sequence;
$xref->{SPECIES_ID} = $species_id;
$xref->{INFO_TYPE} = "SEQUENCE_MATCH";
# TODO synonyms, dependent xrefs etc
push @xrefs, $xref;
}
}
$refseq_io->close();
return \@xrefs;
}
◆ run()
| public XrefParser::RefSeqParser::run | ( | ) |
Undocumented method
Code:
click to view
sub run {
my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $files = $ref_arg->{files};
my $release_file = $ref_arg->{rel_file};
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";
}
$verbose |=0;
my @files = @{$files};
my $peptide_source_id =
$self->get_source_id_for_source_name('RefSeq_peptide', undef, $dbi);
my $mrna_source_id =
$self->get_source_id_for_source_name('RefSeq_mRNA', undef, $dbi);
my $ncrna_source_id =
$self->get_source_id_for_source_name('RefSeq_ncRNA', undef, $dbi);
my $pred_peptide_source_id =
$self->get_source_id_for_source_name('RefSeq_peptide_predicted', undef, $dbi);
my $pred_mrna_source_id =
$self->get_source_id_for_source_name('RefSeq_mRNA_predicted','refseq', $dbi);
my $pred_ncrna_source_id =
$self->get_source_id_for_source_name('RefSeq_ncRNA_predicted', undef, $dbi);
if($verbose){
print "RefSeq_peptide source ID = $peptide_source_id\n";
print "RefSeq_mRNA source ID = $mrna_source_id\n";
print "RefSeq_ncRNA source ID = $ncrna_source_id\n";
print "RefSeq_peptide_predicted source ID = $pred_peptide_source_id\n";
print "RefSeq_mRNA_predicted source ID = $pred_mrna_source_id\n" ;
print "RefSeq_ncRNA_predicted source ID = $pred_ncrna_source_id\n" ;
}
my @xrefs;
foreach my $file (@files) {
my $xrefs =
$self->create_xrefs( $peptide_source_id,
$pred_peptide_source_id,
$mrna_source_id, $ncrna_source_id,
$pred_mrna_source_id, $pred_ncrna_source_id,
$file,
$species_id, $dbi );
if ( !defined($xrefs) ) {
return 1; #error
}
print "Read " . scalar(@$xrefs) ." xrefs from $file\n" if($verbose);
push @xrefs, @{$xrefs};
}
if ( !defined( $self->upload_xref_object_graphs( \@xrefs, $dbi ) ) ) {
return 1; # error
}
if ( defined $release_file ) {
# Parse and set release info.
my $release_io = $self->get_filehandle($release_file);
local $/ = "\n*";
my $release = $release_io->getline();
$release_io->close();
$release =~ s/\s{2,}/ /g;
$release =~
s/.*(NCBI Reference Sequence.*) Distribution Release Notes.*/$1/s;
# Put a comma after the release number to make it more readable.
$release =~ s/Release (\d+)/Release $1,/;
print "RefSeq release: '$release'\n";
$self->set_release( $source_id, $release, $dbi );
$self->set_release( $peptide_source_id, $release, $dbi );
$self->set_release( $mrna_source_id, $release, $dbi );
$self->set_release( $ncrna_source_id, $release, $dbi );
$self->set_release( $pred_peptide_source_id, $release, $dbi );
$self->set_release( $pred_mrna_source_id, $release, $dbi );
$self->set_release( $pred_ncrna_source_id, $release, $dbi );
}
return 0; # successfull
}
The documentation for this class was generated from the following file:
- ensembl/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm
