Merge pull request #290 from ima23/feature/dump_pheno

add dump files for phenotypes plugin script

scripts/export/dump_phenotypes.pl

@@ -0,0 +1,180 @@
+# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+# Copyright [2016-2019] EMBL-European Bioinformatics Institute
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+#      http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# Script to generate an HTML page containing the variant sources of each species
+
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <http://www.ensembl.org/Help/Contact>.
+
+=cut
+
+
+use Bio::EnsEMBL::Registry;
+use Bio::EnsEMBL::VEP::Config;
+use DBI;
+use strict;
+use Getopt::Long;
+use Phenotypes;
+
+###############
+### Options ###
+###############
+my ($output_dir,$e_version,$user,$hname);
+my ($force,$quiet, $species, $help);
+
+## EG options
+my ($site, $etype);
+
+usage() if (!scalar(@ARGV));
+
+GetOptions(
+     'output_dir|o=s'  => \$output_dir,
+     'force|f'         => \$force,
+     'quiet|q'         => \$quiet,
+     "species|s=s"       => \$species,
+     'v=s'             => \$e_version,
+     'user|u=s'        => \$user,
+     'hname=s'         => \$hname,
+     'help!'           => \$help,
+);
+
+if ($help) {
+  usage();
+} elsif (!$e_version) {
+  print STDERR "> Error! Please give an Ensembl version, using the option '-v' \n";
+  usage();
+} elsif (!$output_dir) {
+  print STDERR "> Error! Please give an output directory for the dumps, using the option '-o' \n";
+  usage();
+} elsif (!$user) {
+  print STDERR "> Error! Please give a database user name, using the option '-user' \n";
+  usage();
+} elsif (!$hname) {
+  print STDERR "> Error! Please give the host name where the databases are stored using the option '-hname'\n";
+  usage();
+}
+
+# Settings
+my $database = "";
+
+#VEP-config
+my $cfg = Bio::EnsEMBL::VEP::Config->new({testing => 'hello'});
+#registry data:
+my ($host, $port) = split /\:/, $hname;
+my $registry = 'Bio::EnsEMBL::Registry';
+$registry->load_registry_from_db(
+    -host       => $host,
+    -port       => $port,
+    -user       => $user,
+    -pass       => '',
+    -db_version => $e_version,
+ );
+
+my %only_species = map { $_ => 1 } split(",",$species) if defined $species;
+
+my $sql = qq{SHOW DATABASES LIKE '%variation_$e_version%'};
+my $sth_h = get_connection_and_query($database, $hname, $sql, 1);
+
+my $sqlPF = qq{SELECT count(*) FROM phenotype_feature};
+# Loop over databases
+while (my ($dbname) = $sth_h->fetchrow_array) {
+  next if ($dbname !~ /^[a-z]+_[a-z]+_variation_\d+_\d+$/i);
+  next if ($dbname =~ /^master_schema/ || $dbname =~ /private/);
+
+  $dbname =~ /^(.+)_variation_.+_(.+)/;
+  my $s_name = $1;
+  my $assembly = $2;
+  next if defined $species & !$only_species{$s_name};
+  print STDERR "# $s_name - [ $dbname ]\n";
+
+  ## count phenotype_feature(s)
+  my $sth_pf = get_connection_and_query($dbname, $hname, $sqlPF, 1);
+  my ($count) = $sth_pf->fetchrow_array();
+  print "Found phenotype features: ", $count, "\n";
+  next unless $count > 0;
+
+  my $dumpFile = sprintf($output_dir."/Phenotypes.pm_%s_%i.bed.gz", $s_name, $e_version);
+  $dumpFile = sprintf($output_dir."/Phenotypes.pm_%s_%s.bed.gz", $s_name, $e_version."_GRCh".$assembly) if $s_name eq 'homo_sapiens';
+
+  die ("Phenotype file $dumpFile already exists. Specify a different output folder or use --force to override the existing one\n") if -e $dumpFile & !$force ;
+
+  print "writing: $dumpFile \n" unless $quiet;
+
+  my %reg_config = (reg => $registry, species => $s_name, quiet => $quiet );
+  my %db_config = (config => \%reg_config);
+
+  # Run Phenotypes.pm plugin to export BED formated Phenotypes
+  Phenotypes::generate_phenotype_gff(\%db_config, $dumpFile);
+}
+$sth_h->finish;
+
+
+
+# Connects and execute a query
+sub get_connection_and_query {
+  my $dbname  = shift;
+  my $hname   = shift;
+  my $sql     = shift;
+  my $rtn_sth = shift;
+
+  my ($host, $port) = split /\:/, $hname;
+
+  # DBI connection 
+  my $dsn = "DBI:mysql:$dbname:$host:$port";
+  my $dbh = DBI->connect($dsn, $user) or die "Connection failed";
+
+  my $sth = $dbh->prepare($sql);
+  $sth->execute;
+
+  if ($rtn_sth) {
+    return $sth;
+  }
+  else {
+    $sth->finish;
+  }
+}
+
+
+sub usage {
+
+  print qq{
+  Usage: perl dump_phenotypes.pl [OPTION]
+
+  Dumping to BED of phenotype data for Ensembl Variation species.
+
+  Options:
+
+    -help             Print this message
+
+    -output_dir|o     Output directory for the BED dumps (Required)
+    -force|f          Force to override any pre-existing dumps
+    -quiet|q          Suppress warning messages.Not used by default
+
+    -species|s        Only export the species in the list,
+                        e.g. homo_sapiens,sus_scrofa
+
+    -user|u           Database login user name (Required)
+    -v                Ensembl version, e.g. 96 (Required)
+    -hname            The host name (with port) where the databases are stored,
+                        e.g. ensembldb.ensembl.org1:3334 (Required)
+  } . "\n";
+  exit(0);
+}