module modified to take in some database connection arguments

default behaviour is to use registry and staging, but can also use alternative database on other server

misc-scripts/xref_mapping/XrefParser/RFAMParser.pm

@@ -9,25 +9,65 @@ use base qw( XrefParser::BaseParser );
 use Bio::EnsEMBL::Registry;
 
 
-sub run {
+sub run_script {
 
   my ($self, $ref_arg) = @_;
   my $source_id    = $ref_arg->{source_id};
   my $species_id   = $ref_arg->{species_id};
-  my $files        = $ref_arg->{files};
+  my $file        = $ref_arg->{file};
   my $verbose      = $ref_arg->{verbose};
 
-  if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){
+  if((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
     croak "Need to pass source_id, species_id and file as pairs";
   }
   $verbose |=0;
 
-  my $file = @{$files}[0];
+  my $wget = "";
+  my $user = "ensro";
+  my $host;
+  my $port = 3306;
+  my $dbname;
+  my $pass;
+
+  if($file =~ /wget[=][>](\S+?)[,]/){
+    $wget = $1;
+  }
+  if($file =~ /host[=][>](\S+?)[,]/){
+    $host = $1;
+  }
+  if($file =~ /port[=][>](\S+?)[,]/){
+    $port =  $1;
+  }
+  if($file =~ /dbname[=][>](\S+?)[,]/){
+    $dbname = $1;
+  }
+  if($file =~ /pass[=][>](\S+?)[,]/){
+    $pass = $1;
+  }
+  if($file =~ /user[=][>](\S+?)[,]/){
+    $user = $1;
+  }
+
 
   #get direct RFAM xrefs from core
   my $registry = "Bio::EnsEMBL::Registry";
+  my $dba;
 
-  $registry->load_registry_from_multiple_dbs( 
+  #get the species name
+  my %id2name = $self->species_id2name;
+  my $species_name = $id2name{$species_id}[0];
+
+  if ($host) {
+      $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+         '-host'     => $host,
+         '-user'     => $user,
+         '-pass'     => $pass,
+         '-dbname'   => $dbname,
+         '-species'  => $species_name,
+         '-group'    => 'core',
+       );
+  } else {
+      $registry->load_registry_from_multiple_dbs( 
       {
         '-host'    => 'ens-staging1',
         '-user'    => 'ensro',
@@ -36,13 +76,9 @@ sub run {
         '-host'     => 'ens-staging2',
         '-user'     => 'ensro',
       },
-  );
-
-  #get the species name
-  my %id2name = $self->species_id2name;
-  my $species_name = $id2name{$species_id}[0];
-
-  my $dba = $registry->get_DBAdaptor($species_name, 'core');
+      );
+      $dba = $registry->get_DBAdaptor($species_name, 'core');
+  }
 
   my $rfam_sql = "select distinct t.stable_id, hit_name from analysis a join transcript t on (a.analysis_id = t.analysis_id and a.logic_name = 'ncRNA' and t.biotype != 'miRNA') join exon_transcript et on (t.transcript_id = et.transcript_id) join supporting_feature sf on (et.exon_id = sf.exon_id and sf.feature_type = 'dna_align_feature' ) join dna_align_feature df on (sf.feature_id = df.dna_align_feature_id) order by hit_name";
 
@@ -64,59 +100,52 @@ sub run {
   }
   $sth->finish;     
 
-  my $file_io = $self->get_filehandle($file);
-  if ( !defined $file_io ) {
-    print STDERR "ERROR: Could not open $file\n";
-    return 1;    # 1 is an error
+  my $ua = LWP::UserAgent->new();
+  $ua->timeout(10);
+  $ua->env_proxy();
+  my $request = HTTP::Request->new(GET => $wget);
+  my $response = $ua->request($request);
+
+  if ( !$response->is_success() ) {
+    warn($response->status_line);
+    return 1;
   }
+  my @lines = split(/\n\n/, $response->decoded_content);
 
   my @xrefs;
+  my $xref_count = 0;
+  my $direct_count = 0;
 
-  local $/ = "//\n";
-
-
-  my $xref_count;
-  my $direct_count;
-
-  while ($_ = $file_io->getline()) {
+  while (my $entry = shift @lines) {
 
     my $xref;
-
-    my $entry = $_;
     chomp $entry;
-
     next if (!$entry);
 
-    my ($accession) = $entry =~ /\n#=GF\sAC\s+(\w+)/;
-    my ($label) = $entry =~ /\n#=GF\sID\s+([^\n]+)/;
+    my ($accession) = $entry =~ /#=GF\sAC\s+(\w+)/ ;
+    my ($label) = $entry =~ /\n#=GF\sID\s+([^\n]+)/; 
     my ($description) = $entry =~ /\n#=GF\sDE\s+([^\n]+)/;
-
-    if (exists($rfam_transcript_stable_ids{$accession})){
-
-	#add xref
-	my $xref_id = $self->add_xref({ acc        => $accession,
-				      version    => 0,
+    if ($accession) {
+      if (exists($rfam_transcript_stable_ids{$accession})){
+      #add xref
+        my $xref_id = $self->add_xref({ acc      => $accession,
+  				      version    => 0,
 				      label      => $label || $accession ,
 				      desc       => $description,
 				      source_id  => $source_id,
 				      species_id => $species_id,
 				      info_type  => "DIRECT"} );
 
-	my @transcript_stable_ids = @{$rfam_transcript_stable_ids{$accession}};
-
-	foreach my $stable_id (@transcript_stable_ids){
-	    $self->add_direct_xref($xref_id, $stable_id, "Transcript", "");
-	    $direct_count++;
-	}	
-
-      $xref_count++;
-
+        my @transcript_stable_ids = @{$rfam_transcript_stable_ids{$accession}};
+        foreach my $stable_id (@transcript_stable_ids){
+           $self->add_direct_xref($xref_id, $stable_id, "Transcript", "");
+           $direct_count++;
+         }	
+         $xref_count++;
+      }
     }
-
   }
 
-  $file_io->close();
-
   print "Added $xref_count RFAM xrefs and $direct_count direct xrefs\n" if($verbose);
   if ( !$xref_count ) {
       return 1;    # 1 error