logging improvements

modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm

@@ -152,10 +152,15 @@ sub map_stable_ids {
   # generate a new mapping_session and write all mapping_session data to a file
   $self->generate_mapping_session;
 
+  $self->logger->info("== Stable ID mapping for $type...\n\n", 0, 'stamped');
+
   # 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') };
-  return unless (scalar(keys %all_sources));
+  unless (scalar(keys %all_sources)) {
+    $self->logger->info("No cached ${type}s found.\n\n");
+    return;
+  }
 
   my %stats = map { $_ => 0 }
     qw(mapped_known mapped_novel new lost_known lost_novel);
@@ -313,6 +318,7 @@ sub map_stable_ids {
   # also generate and write stats to file
   $self->generate_mapping_stats($type, \%stats);
 
+  $self->logger->info("Done.\n\n");
 }
 
 
@@ -624,15 +630,15 @@ sub write_stable_ids_to_file {
     # check for missing created and modified dates
     my $created_date = $obj->created_date;
     unless ($created_date) {
-      $self->logger->debug("Missing created_date for target ".
-        $obj->to_string."\n", 1);
+      #$self->logger->debug("Missing created_date for target ".
+      #  $obj->to_string."\n", 1);
       $created_date = $self->mapping_session_date;
     }
     
     my $modified_date = $obj->modified_date;
     unless ($modified_date) {
-      $self->logger->debug("Missing modified_date for target ".
-        $obj->to_string."\n", 1);
+      #$self->logger->debug("Missing modified_date for target ".
+      #  $obj->to_string."\n", 1);
       $modified_date = $self->mapping_session_date;
     }
     

modules/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm

@@ -52,7 +52,7 @@ sub score_transcripts {
     throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
   }
 
-  $self->logger->info("Starting transcript scoring...\n\n", 0, 'stamped');
+  $self->logger->info("-- Scoring transcripts...\n\n", 0, 'stamped');
 
   # build scores based on exon scores
   my $matrix = $self->scores_from_exon_scores($exon_matrix);
@@ -65,15 +65,9 @@ sub score_transcripts {
   $self->logger->info(sprintf($fmt, "Total source transcripts:",
     $self->cache->get_count_by_name('transcripts_by_id', 'source')), 1);
 
-  $self->logger->info(sprintf($fmt, "Scored source transcripts:",
-    $matrix->get_source_count), 1);
-
   $self->logger->info(sprintf($fmt, "Total target transcripts:",
     $self->cache->get_count_by_name('transcripts_by_id', 'target')), 1);
 
-  $self->logger->info(sprintf($fmt, "Scored target transcripts:",
-    $matrix->get_target_count), 1);
-
   $self->log_matrix_stats($matrix);
   
   $self->logger->info("\nDone with transcript scoring.\n\n");
@@ -162,6 +156,7 @@ sub flag_matrix_from_exon_scores {
   my $i;
   my $num_transcripts =
     scalar(keys %{ $self->cache->get_by_name('transcripts_by_id', 'source') });
+  my $progress_id = $self->logger->init_progress($num_transcripts, 100);
 
   $self->logger->info("Creating flag matrix...\n", 1);
 
@@ -169,7 +164,7 @@ sub flag_matrix_from_exon_scores {
   foreach my $source_transcript (values %{ $self->cache->get_by_name('transcripts_by_id', 'source') }) {
     
     # log progress
-    $self->logger->log_progress($num_transcripts, ++$i, 20, 1, 0);
+    $self->logger->log_progress($progress_id, ++$i, 1);
 
     # get all exons for the source transcript
     foreach my $source_exon (@{ $source_transcript->get_all_Exons }) {
@@ -222,6 +217,7 @@ sub score_matrix_from_flag_matrix {
   my $i;
   my $num_transcripts =
     scalar(keys %{ $self->cache->get_by_name('transcripts_by_id', 'source') });
+  my $progress_id = $self->logger->init_progress($num_transcripts, 100);
 
   $self->logger->info("Creating score matrix from flag matrix...\n", 1);
   
@@ -229,7 +225,7 @@ sub score_matrix_from_flag_matrix {
   foreach my $source_transcript (values %{ $self->cache->get_by_name('transcripts_by_id', 'source') }) {
     
     # log progress
-    $self->logger->log_progress($num_transcripts, ++$i, 20, 1, 0);
+    $self->logger->log_progress($progress_id, ++$i, 1);
 
     # We are only interested in scoring with exons that are in the target
     # transcript. The scored mapping matrix may contain scores for exons that
@@ -262,8 +258,8 @@ sub score_matrix_from_flag_matrix {
 
           next unless ($target_exons{$target_exon_id});
 
-          my $score = $exon_matrix->get_score(
-            $source_exon->id, $target_exon_id);
+          my $score = $exon_matrix->get_score($source_exon->id,
+            $target_exon_id);
           $max_source_score = $score if ($score > $max_source_score);
         }