/usr/share/perl5/GO/Handlers/obo_godb_flat.pm is in libgo-perl 0.15-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#
# This GO module is maintained by Chris Mungall <cjm@fruitfly.org>
#
# see also - http://www.geneontology.org
# - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself
=head1 NAME
GO::Handlers::obo_godb_flat - transforms OBO XML to MySQL tables
=head1 SYNOPSIS
use GO::Handlers::obo_godb_flat
=cut
=head1 DESCRIPTION
transforms OBO XML events into flat tables for mysql to load
part of the association bulk loading pipeline
=head1 PUBLIC METHODS -
=cut
# makes objects from parser events
package GO::Handlers::obo_godb_flat;
use Data::Stag qw(:all);
use Data::Dumper;
use GO::Parsers::ParserEventNames;
use base qw(GO::Handlers::base);
use strict qw(vars refs);
use constant DELIMITER => "\t"; # separates fields
sub init {
my $self = shift;
$self->SUPER::init();
$self->{tables} = {
dbxref => [ qw(id xref_dbname xref_key xref_keytype xref_desc) ], # must append many dbxrefs
term => [ qw(id name term_type acc is_obsolete is_root is_relation) ], # must append SO terms, qualifiers
gene_product => [ qw(id symbol dbxref_id species_id type_id full_name) ],
association => [ qw(id term_id gene_product_id is_not role_group assocdate source_db_id) ],
db => [ qw(id name fullname datatype generic_url url_syntax url_example uri_prefix) ], # last 4 all null in current load
evidence => [ qw(id code association_id dbxref_id seq_acc) ],
association_qualifier => [ qw(id association_id term_id value) ], # must append
species => [ qw(id ncbi_taxa_id common_name lineage_string genus species parent_id left_value right_value taxonomic_rank) ],
# linking tables
gene_product_synonym => [ qw(gene_product_id product_synonym)],
evidence_dbxref => [ qw(evidence_id dbxref_id) ],
association_species_qualifier => [ qw(id association_id species_id) ],
};
$self->{fhs} = { map (("$_.txt" => 0), keys %{$self->{tables}}) };
$self->{pk} = { map (($_ => 0), keys %{$self->{tables}} ) };
}
sub apph {
my $self = shift;
$self->{apph} = shift if @_;
return $self->{apph};
}
sub _obo_escape {
my $s=shift;
$s =~ s/\\/\\\\/;
$s =~ s/([\{\}])/\\$1/g;
$s;
}
sub safe {
my $word = shift;
$word =~ s/ /_/g;
$word =~ s/\-/_/g;
$word =~ s/\'/prime/g;
$word =~ tr/a-zA-Z0-9_//cd;
$word =~ s/^([0-9])/_$1/;
$word;
}
sub quote {
my $word = shift;
#$word =~ s/,/\\,/g; ## no longer required
$word =~ s/\"/\\\"/g;
"\"$word\"";
}
sub e_prod {
my $self = shift;
my $prod = shift;
my $proddb = $self->up_to('dbset')->get_proddb;
# $self->file('gene_product.txt'); done in add_gene_product
my $gp_id = $self->add_gene_product($prod, $proddb);
my @assocs = $prod->get_assoc;
for my $assoc (@assocs) {
# first dump the ASSOCIATION table
$self->dump_table('association', [
++$self->{pk}{association},
$self->get_term_id($assoc->get_termacc),
$gp_id,
stag_get($assoc, IS_NOT),
'\N', # role_group current always NULL
$assoc->sget_assocdate,
$self->get_sourcedb_id($assoc->sget_source_db)
]);
# now the qualifiers
for my $qual ($assoc->get_qualifier) {
$self->dump_table('association_qualifier', [
++$self->{pk}{association_qualifier},
$self->{pk}{association},
$self->get_term_id($qual, 'association_qualifier'),
'\N', # value is currently always NULL
]);
}
# get species qualifier for dual taxon species
for my $species_qual ($assoc->get_species_qualifier) {
$self->dump_table('association_species_qualifier', [
++$self->{pk}{association_species_qualifier},
$self->{pk}{association},
$self->get_taxon_id($species_qual),
]);
}
# now evidence and evidence dbxref
for my $ev ($assoc->get_evidence) {
# prioritize PMIDs
my ($ref) = grep {$_ =~ /^PMID/} $ev->get_ref();
if (!$ref) {
$ref = $ev->sget_ref;
}
$self->dump_table('evidence', [
++$self->{pk}{evidence},
$ev->sget_evcode,
$self->{pk}{association},
$self->get_dbxref_id($ref), # only the first one here
$ev->sget_with || "", # put only the first one here, I dunno why
]);
for my $ref ($ev->get_ref) {
next; # skip whole loop until we figure this out.
$self->dump_table('evidence_dbxref', [
$self->{pk}{evidence},
$self->get_dbxref_id($ref),
]);
}
for my $with ($ev->get_with) {
$self->dump_table('evidence_dbxref', [
$self->{pk}{evidence},
$self->get_dbxref_id($with),
]);
}
}
}
}
sub add_gene_product {
my $self = shift;
my $prod = shift;
my $proddb = shift;
my $acc = $prod->get_prodacc;
if ($self->apph->dbxref2gpid_h->{uc($proddb)}->{uc($acc)}) {
# check to see if we've already added it
# unique key for gene product is actually dbxref_id, but need the gp_id
} else {
# warn "$proddb, $acc, does not exist, creating";
# if not, write a line to gene_product.txt
# new dbxref_id is added by get_dbxref_id.
$self->dump_table('gene_product', [
++$self->{pk}{gene_product},
$prod->sget_prodsymbol,
$self->get_dbxref_id($proddb, $acc),
$self->get_taxon_id($prod->get_prodtaxa),
# '\N', # currently no secondary species ids
$self->get_term_id($prod->get_prodtype, 'sequence'),
$prod->sget_prodname || "", # that should be full name.
]);
$self->apph->dbxref2gpid_h->{uc($proddb)}->{uc($acc)} = $self->{pk}{gene_product};
# add synoyms if necessary
for my $syn ($prod->get_prodsyn) {
$self->dump_table('gene_product_synonym', [
$self->{pk}{gene_product},
$syn,
]);
}
}
return $self->apph->dbxref2gpid_h->{uc($proddb)}->{uc($acc)};
}
sub get_dbxref_id {
my $self = shift;
my $dbname = shift;
my $key = shift;
if (!$key) {
if ($dbname =~ /^([^:]+):+(\S+)/) {
$dbname = $1;
$key = $2;
}
}
if (!$dbname || !$key) {
warn "Must supply dbname and key: ($dbname),($key) attempting to write $self->{_file}\n";
return 0;
}
my $ucKey = uc($key);
my $ucDb = uc($dbname);
# mysql will handle case-insensitivity, but perl keeps seperate
return $self->apph->dbxref2id_h->{$ucDb}->{$ucKey} if $self->apph->dbxref2id_h->{$ucDb}->{$ucKey};
# doesn't exist, add it to dbxref file and hash
my $oldfile = $self->file;
$self->dump_table('dbxref', [
++$self->{pk}{dbxref},
$dbname,
$key,
'\N',
'\N',
]);
$self->file($oldfile); # set filename back
$self->apph->dbxref2id_h->{$ucDb}->{$ucKey} = $self->{pk}{dbxref}; # return the id
}
sub get_term_id {
# note this hopeless fails if 2 terms in different CVs have the same name!
my $self = shift;
my $term = shift;
my $termType = shift;
my $acc = shift || $term;
$term = lc($term) unless $term =~ /^GO:/; # sometimes people use Gene instead of gene
return $self->apph->acc2id_h->{$term} if $self->apph->acc2id_h->{$term};
die "No term type specified for $term, and not in hash" if !$termType;
# doesn't exist, add it to dbxref file and hash
my $oldfile = $self->file;
$self->dump_table('term', [
++$self->{pk}{term},
$term,
$termType,
$acc,
0, # never is_obsolete
0, # never is_root
0, # never a relationship type
]);
$self->file($oldfile); # set file name back;
$self->apph->acc2id_h->{$term} = $self->{pk}{term}; # return the id
}
sub get_sourcedb_id {
my $self = shift;
my $db = shift;
return $self->apph->source2id_h->{uc($db)} if $self->apph->source2id_h->{uc($db)};
# doesn't exist, add it to file and hash
my $oldfile = $self->file;
$self->dump_table('db', [
++$self->{pk}{db},
$db,
'\N',
'\N',
'\N',
'\N',
'\N',
'\N',
]);
$self->file($oldfile); # set file name back
$self->apph->source2id_h->{uc($db)} = $self->{pk}{db}; # return the id
}
sub get_taxon_id {
my $self = shift;
my $taxonId = shift || '';
return $self->apph->taxon2id_h->{$taxonId} if $self->apph->taxon2id_h->{$taxonId};
warn "Could not find id in db for taxon $taxonId, adding\n";
my $oldfile = $self->file;
$self->dump_table('species', [
++$self->{pk}{species},
$taxonId,
'\N', # name unknown
'\N', # lineage unknown
'\N', # genuss unknown
'\N', # species unknown
'\N', # parent_id unknown
'\N', # left unknown
'\N', # right unknown
'\N', # taxonomic rank unknown
]);
$self->file($oldfile); # set file name back;
$self->apph->taxon2id_h->{$taxonId} = $self->{pk}{species}; # return the id
}
sub file {
# overrides Data::Stag::Writer file
# with no arguments, returns current filename
# with argument, sets file handle to file handle from {fhs} hash
# if file handle not open, opens with safe_fh
# returns "new" file name.
my $self = shift;
my $fh = $self->{fhs}; # hash of filehandles
# create the keys if they don't exist, suppresses warnings
# first time this is called, might be STDOUT or something
$self->{_file} = undef unless $self->{_file};
$self->{_fh} = undef unless $self->{_fh};
if (@_) {
$self->{_file} = shift;
$self->{_fh} = undef;
}
if ( !$self->{_file} || !$fh->{$self->{_file}} ) {
# print STDERR "opening file $self->{_file}...\n";
$fh->{$self->{_file}} = $self->safe_fh;
}
$self->{_fh} = $fh->{$self->{_file}} if exists $self->{_file};
return $self->{_file};
}
sub close_files {
my $self = shift;
for my $fh (values %{$self->{fhs}}) {
close($fh) if $fh && $fh ;
}
# close($self->{_fh}) if $self->{_fh};
}
sub tables {
$_[0]->{tables};
}
sub dump_table {
my $self = shift;
my $tab = shift;
my $fieldsRef = shift;
die "Don't know anything about $tab" if ( !$self->{tables}->{$tab} || !scalar (@{ $self->{tables}->{$tab} }) );
die "Tried to write wrong number of fields $tab" if scalar(@$fieldsRef) != scalar(@{ $self->{tables}->{$tab} });
$self->file("$tab.txt");
$self->write(join(DELIMITER, @$fieldsRef));
$self->write("\n");
}
1;
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