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executable file 115 lines (87 sloc) 2.276 kb
#!/usr/local/bin/perl5.6.1
use strict;
BEGIN
{
# my $configFile = "/nfs/pathdb/dev/go-cgi/config.pl";
my $configFile = "/nfs/pathdb/amigo/conf/config.pl";
if (-f $configFile)
{
require $configFile;
}
}
use Getopt::Long;
my $associations;
my $definition;
&GetOptions("assoc" => \$associations,
"def" => \$definition);
use GO::AppHandle;
if(@ARGV == 0)
{
print "USAGE: go -def -assoc acc\n"; exit 0;
}
my $acc_num = $ARGV[0];
my $dbname = $ENV{GO_DBNAME};
my $dbport = $ENV{GO_DBPORT};
my $dbhost = $ENV{GO_DBHOST};
my $dbuser = $ENV{GO_DBUSER};
my $dbauth = $ENV{GO_DBAUTH};
if (not $dbname =~ /^go/) {
print STDERR "GO database name uncorrect, must start 'go...' !!";
exit 1;
}
my $apph = GO::AppHandle->connect (
-dbname => $dbname,
-dbport => $dbport,
-dbhost => $dbhost,
-dbuser => $dbuser,
-dbauth => $dbauth,
)
or die "can't connect to GO database, $dbname!!!\n";
#my @accs = qw(O00221);
my @accs;
push(@accs, $acc_num);
my @pqlist = map { {acc=>$_} } @accs;
my $term_l = $apph->get_terms({products=>[@pqlist]});
foreach my $term (@$term_l)
{
my $type = $term->term_type;
if($type =~ m/_component/i)
{
printf "/GO_component=\"";
}
elsif($type =~ m/_function/i)
{
printf "/GO_function=\"";
}
elsif($type =~ m/_process/i)
{
printf "/GO_process=\"";
}
printf "%s (%s);", $term->acc, $term->name;
if($associations)
{
foreach my $assoc (@{$term->selected_association_list || []})
{
my $gp = $assoc->gene_product;
my $ev_l = $assoc->evidence_list || [];
printf " %s; %s:%s", $assoc->evidence_as_str, $gp->speciesdb, $gp->acc;
foreach my $syn (@{$gp->synonym_list || []})
{
print " ($syn)";
}
printf ";";
printf " db_xref=";
foreach my $ref (@{$term->dbxref_list || []})
{
printf "%s", $ref->as_str;
}
printf ";";
}
}
if($definition)
{
printf " %s;", $term->definition;
}
# printf "Synonyms:%s\n", join(", ", @{$term->synonym_list});
print "\n";
}
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