Add patches from Dan S. to allow the stable ID mapping pipeline to run

on new species (i.e. species without previous stable IDs).

Untested at the moment.

modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm

@@ -678,6 +678,34 @@ sub non_mapped_transcript_rescore {
     my @target_transcripts = @{ $self->cache->get_by_key(
       'transcripts_by_exon_id', 'target', $entry->target) };
 
+    # EG reworking of logic to allow no source/target e.g. for new
+    # species in multispecies databases
+    my $st =
+      $self->cache()
+      ->get_by_key( 'transcripts_by_exon_id', 'source',
+                    $entry->source() );
+    my @source_transcripts;
+    if ( !defined($st) ) {
+      $self->logger->warning(
+                          "Can't find source transcipts by exon_id for "
+                            . $entry->source() );
+    } else {
+      @source_transcripts = @{$st};
+    }
+
+    my $tt =
+      $self->cache()
+      ->get_by_key( 'transcripts_by_exon_id', 'target',
+                    $entry->target() );
+    my @target_transcripts = ();
+    if ( !defined($tt) ) {
+      $self->logger->warning(
+                          "Can't find target transcipts by exon_id for "
+                            . $entry->target() );
+    } else {
+      @target_transcripts = @{$tt};
+    }
+
     my $found_mapped = 0;
 
     TR:

modules/Bio/EnsEMBL/IdMapping/ResultAnalyser.pm

@@ -733,28 +733,33 @@ sub create_summary_email {
 
   print $fh "\n";
 
-  #
-  # clicklist of first 10 deleted genes
-  #
-  print $fh qq(\nFirst 10 deleted known genes:\n);
-  print $fh qq(=============================\n\n);
+  # EG genes_lost.txt file may not exist if species is new
+  if ( $self->file_exists( 'genes_lost.txt', 'debug' ) ) {
+    #
+    # clicklist of first 10 deleted genes
+    #
 
-  my $in_fh = $self->get_filehandle( 'genes_lost.txt', 'debug', '<' );
-  my $prefix = $self->conf->param('urlprefix');
-  my $i;
+    print $fh qq(\nFirst 10 deleted known genes:\n);
+    print $fh qq(=============================\n\n);
 
-  while (<$in_fh>) {
-    last if ( ++$i > 10 );
+    my $in_fh = $self->get_filehandle( 'genes_lost.txt', 'debug', '<' );
+    my $prefix = $self->conf->param('urlprefix');
+    my $i;
 
-    chomp;
-    my ( $stable_id, $type ) = split(/\s+/);
+    while (<$in_fh>) {
+      last if ( ++$i > 10 );
 
-    next unless ( $type eq 'known' );
+      chomp;
+      my ( $stable_id, $type ) = split(/\s+/);
 
-    print $fh sprintf( $fmt2, $stable_id, "${prefix}$stable_id" );
-  }
+      next unless ( $type eq 'known' );
+
+      print $fh sprintf( $fmt2, $stable_id, "${prefix}$stable_id" );
+    }
+
+    close($in_fh);
+  } ## end if ( $self->file_exists...)
 
-  close($in_fh);
   close($fh);
 }
 

modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm

@@ -120,30 +120,41 @@ sub initial_stable_id {
   my $self = shift;
   my $type = shift;
 
-  my $init_stable_id;
-
-  # use stable ID from configuration if set
-  if ($init_stable_id = $self->conf->param("starting_${type}_stable_id")) {
-    $self->logger->debug("Using pre-configured $init_stable_id as base for new $type stable IDs.\n");
-    return $init_stable_id;
-  }
-
-  my $s_dba = $self->cache->get_DBAdaptor('source');
-  my $s_dbh = $s_dba->dbc->db_handle;
-
-  # look in the ${type}_stable_id table first
-  my $sql = qq(SELECT MAX(stable_id) FROM ${type}_stable_id);
-  $init_stable_id = $self->fetch_value_from_db($s_dbh, $sql);
+  # EG modifications to permit the current stable ID to persist trohough
+  # different invocations
+  my $init_stable_id = $self->{stable_id_list}{$type};
+
+  if ( !defined($init_stable_id) ) {
+    # use stable ID from configuration if set
+    if ( $init_stable_id =
+         $self->conf->param("starting_${type}_stable_id") )
+    {
+      $self->logger->debug(   "Using pre-configured $init_stable_id "
+                            . "as base for new $type stable IDs.\n" );
+      return $init_stable_id;
+    }
 
-  # also look in gene_archive to make sure there are no larger Ids there
-  unless ($type eq 'exon') {
-    $sql = qq(SELECT MAX(${type}_stable_id) FROM gene_archive);
-    my $archived_stable_id = $self->fetch_value_from_db($s_dbh, $sql);
-    if ($archived_stable_id and $self->is_valid($archived_stable_id) and
-        ($archived_stable_id gt $init_stable_id)) {
-      $init_stable_id = $archived_stable_id;
+    my $s_dba = $self->cache->get_DBAdaptor('source');
+    my $s_dbh = $s_dba->dbc->db_handle;
+
+    # look in the ${type}_stable_id table first
+    my $sql = qq(SELECT MAX(stable_id) FROM ${type}_stable_id);
+    $init_stable_id = $self->fetch_value_from_db( $s_dbh, $sql );
+
+    # also look in gene_archive to make sure there are no larger Ids
+    # there
+    unless ( $type eq 'exon' ) {
+      $sql = qq(SELECT MAX(${type}_stable_id) FROM gene_archive);
+      my $archived_stable_id =
+        $self->fetch_value_from_db( $s_dbh, $sql );
+      if (     $archived_stable_id
+           and $self->is_valid($archived_stable_id)
+           and ( $archived_stable_id gt $init_stable_id ) )
+      {
+        $init_stable_id = $archived_stable_id;
+      }
     }
-  }
+  } ## end if ( !defined($init_stable_id...))
 
   if ($init_stable_id) {
     # since $init_stable_id now is the highest existing stable Id for this

modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm

@@ -187,9 +187,10 @@ sub map_stable_ids {
   # check if there are any objects of this type at all
   my %all_sources = %{ $self->cache->get_by_name("${type}s_by_id", 'source') };
   my %all_targets = %{ $self->cache->get_by_name("${type}s_by_id", 'target') };
-  unless (scalar(keys %all_sources)) {
-    $self->logger->info("No cached ${type}s found.\n\n");
-    return;
+  if ( scalar( keys(%all_sources) ) == 0 ) {
+    # EG may be possible to have no sources for new species
+    $self->logger->warning("No cached ${type}s found.\n\n");
+    %all_sources = ();
   }
 
   my %stats = map { $_ => 0 }
@@ -637,24 +638,31 @@ sub generate_mapping_stats {
   my $novel_total = $stats->{'mapped_novel'} + $stats->{'lost_novel'};
 
   # no split into known and novel for exons
-  unless ( $type eq 'exon' ) {
-    $result .= sprintf( $fmt2,
-	'known',
-	$stats->{'mapped_known'},
-	$stats->{'lost_known'},
-	($known_total ? $stats->{'mapped_known'}/$known_total*100 : 0)
-    );
+  if ( $type ne 'exon' ) {
+    $result .= sprintf( $fmt2, 'known',
+                        $stats->{'mapped_known'},
+                        $stats->{'lost_known'}, (
+                            $known_total
+                          ? $stats->{'mapped_known'}/$known_total*100
+                          : 0 ) );
+
+    $result .= sprintf( $fmt2, 'novel',
+                        $stats->{'mapped_novel'},
+                        $stats->{'lost_novel'}, (
+                            $novel_total
+                          ? $stats->{'mapped_novel'}/$novel_total*100
+                          : 0 ) );
+  }
 
+  if ( $mapped_total == 0 ) {
+    # EG different calculation needed when no mappings found for new
+    # species
+    $result .= sprintf( $fmt2, 'total', $mapped_total, $lost_total, 0 );
+  } else {
     $result .= sprintf( $fmt2,
-	'novel',
-	$stats->{'mapped_novel'},
-	$stats->{'lost_novel'},
-	($novel_total ? $stats->{'mapped_novel'}/$novel_total*100 : 0)
-    );
-  } ## end unless ( $type eq 'exon' )
-
-  $result .= sprintf($fmt2, 'total', $mapped_total, $lost_total,
-    $mapped_total/($known_total + $novel_total)*100);
+                    'total', $mapped_total, $lost_total,
+                    $mapped_total/( $known_total + $novel_total )*100 );
+  }
 
   # log result
   $self->logger->info($result."\n");

modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm

@@ -376,12 +376,15 @@ sub rescore_gene_matrix_lsf {
       is_component  => 1,
   );
 
-  my $cmd = qq{$Bin/synteny_rescore.pl $options --index \$LSB_JOBINDEX};
-
-  my $pipe = qq{|bsub -J$lsf_name\[1-$num_jobs\] } .
-    qq{-o $logpath/synteny_rescore.\%I.out } .
-    qq{-e $logpath/synteny_rescore.\%I.err } .
-    $self->conf->param('lsf_opt_synteny_rescore');
+  my $cmd = qq{perl -I./modules $Bin/synteny_rescore.pl }
+    . qq{$options --index \$LSB_JOBINDEX};
+
+  my $pipe =
+      qq{|bsub -J$lsf_name\[1-$num_jobs\] }
+    . qq{-o $logpath/synteny_rescore.\%I.out }
+    . qq{-e $logpath/synteny_rescore.\%I.err }
+    . $self->conf()->param('lsf_opt_run')
+    . $self->conf()->param('lsf_opt_synteny_rescore');
 
   # run lsf job array
   $self->logger->info("Submitting $num_jobs jobs to lsf.\n");