Merge pull request #513 from dozy/spatial_filter_stats_parsing_update

update parsing of spatial filter stats in spatial_filter QC check

.travis.yml

@@ -19,6 +19,8 @@ dist:
 
 addons:
   postgresql: "9.3"
+  apt:
+    update: true
 
 env:
   global:

Changes

@@ -1,5 +1,7 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+ - update parsing of spatial filter stats in spatial_filter QC check
+
 release 64.6.2
  - QC viewer changes for genotype call
 

lib/npg_qc/autoqc/results/spatial_filter.pm

@@ -32,12 +32,12 @@ has 'num_spatial_filter_fail_reads'=> (
 sub parse_output{
   my ( $self, $stderr_output ) = @_;
 
-#Processed 419675538 traces
-#QC failed        0 traces
+# expected format: "Total Processed 943540734     Failed 4338894 traces"
 
   my $log = slurp defined $stderr_output ? $stderr_output : \*STDIN;
-  if($log=~/^Processed \s+ (\d+) \s+ traces$/smx) {$self->num_total_reads($1);}
-  if($log=~/^(?:QC[ ]failed|Removed) \s+ (\d+) \s+ traces$/smx) {$self->num_spatial_filter_fail_reads($1);}
+  my ($total, $fail) = ($log =~ /^Total \t Processed \s+ (\d+) \s+ Failed \s+ (\d+) \s+ traces$/smx);
+  $self->num_total_reads($total);
+  $self->num_spatial_filter_fail_reads($fail);
 
   return;
 }

t/60-autoqc-results-spatial_filter.t

@@ -13,15 +13,16 @@ my $tempdir = tempdir( CLEANUP => 1);
 {
     my $r = npg_qc::autoqc::results::spatial_filter->new(
                                        position => 1,
-                                       id_run   => 8926,
+                                       id_run   => 25810,
                                  );
     isa_ok ($r, 'npg_qc::autoqc::results::spatial_filter');
 
-    my $stats_output_string = slurp 't/data/autoqc/PB_cal_score_8926_1_20121209-190404.494308.out';
+    my $stats_output_string = slurp 't/data/autoqc/25810_1.bam.filter.stats';
+
     $r->parse_output(\$stats_output_string);    
 
-    is($r->num_total_reads, 2*209837769, 'total reads');    
-    is($r->num_spatial_filter_fail_reads, 0, 'spatial filter fail reads');    
+    is($r->num_total_reads, 629464762, 'total reads');    
+    is($r->num_spatial_filter_fail_reads, 42, 'spatial filter fail reads');    
 
     lives_ok {
       $r->freeze();
@@ -30,7 +31,7 @@ my $tempdir = tempdir( CLEANUP => 1);
 
     is ($r->composition->num_components, 1, 'one component');
     my $component = $r->composition->get_component(0);
-    is ($component->id_run, 8926, 'component id_run');
+    is ($component->id_run, 25810, 'component id_run');
     is ($component->position, 1, 'component position');
     ok (!$component->has_tag_index, 'component tag index has not been set');
     is ($component->tag_index, undef, 'component tag index is undefined');
@@ -39,31 +40,31 @@ my $tempdir = tempdir( CLEANUP => 1);
 {
     my $r = npg_qc::autoqc::results::spatial_filter->new(
                                        position => 2,
-                                       id_run   => 8926,
+                                       id_run   => 25810,
                                  );
 
     open my $stats_output_fh, '<',
-      't/data/autoqc/PB_cal_score_8926_2_20121209-190404.494309.out' or croak 'fail to open fh';
+      't/data/autoqc/25810_2.bam.filter.stats' or croak 'fail to open fh';
     lives_ok {
       local *STDIN=$stats_output_fh;
       $r->parse_output();
     } 'parse from (pseudo) stdin';
     close $stats_output_fh or croak 'fail to close fh';    
 
-    is($r->num_total_reads, 439161826, 'total reads');    
-    is($r->num_spatial_filter_fail_reads, 358824, 'spatial filter fail reads');    
+    is($r->num_total_reads, 649612652, 'total reads');    
+    is($r->num_spatial_filter_fail_reads, 1024, 'spatial filter fail reads');    
 
     lives_ok {
       $r->freeze();
       $r->store($tempdir);
     } 'no error when save data into json (store passed directory)';
 
-    my $hash = from_json( slurp qq{$tempdir/8926_2.spatial_filter.json} );
+    my $hash = from_json( slurp qq{$tempdir/25810_2.spatial_filter.json} );
 
     my $expected_hash_structure = {
-      'num_total_reads' => 439161826,
-      'num_spatial_filter_fail_reads' => 358824,
-      'id_run' => 8926,
+      'num_total_reads' => 649612652,
+      'num_spatial_filter_fail_reads' => 1024,
+      'id_run' => 25810,
       'info' => {},
       'position' => 2,
     };
@@ -94,30 +95,31 @@ my $tempdir = tempdir( CLEANUP => 1);
 {
     my $r = npg_qc::autoqc::results::spatial_filter->new(
                                        position => 4,
-                                       id_run   => 8926,
+                                       id_run   => 25810,
                                  );
     open my $stats_output_fh, '<',
-      't/data/autoqc/PB_cal_score_8926_4_20121209-190404.494309.out' or croak 'fail to open fh';
+      't/data/autoqc/25810_4.bam.filter.stats' or croak 'fail to open fh';
+
     lives_ok {
       local *STDIN=$stats_output_fh;
       $r->parse_output();
     } 'parse from (pseudo) stdin';
     close $stats_output_fh or croak 'fail to close fh';
 
-    is($r->num_total_reads, 439161826, 'total reads');
-    is($r->num_spatial_filter_fail_reads, 358824, 'spatial filter fail reads');
+    is($r->num_total_reads, 653495042, 'total reads');
+    is($r->num_spatial_filter_fail_reads, 115390, 'spatial filter fail reads');
 
     lives_ok {
       $r->freeze();
       $r->store($tempdir);
     } 'no error when save data into json (store passed directory)';
 
-    my $hash = from_json( slurp qq{$tempdir/8926_4.spatial_filter.json} );
+    my $hash = from_json( slurp qq{$tempdir/25810_4.spatial_filter.json} );
 
     my $expected_hash_structure = {
-      'num_total_reads' => 439161826,
-      'num_spatial_filter_fail_reads' => 358824,
-      'id_run' => 8926,
+      'num_total_reads' => 653495042,
+      'num_spatial_filter_fail_reads' => 115390,
+      'id_run' => 25810,
       'info' => {},
       'position' => 4,
     };

t/data/autoqc/25810_1.bam.filter.stats

@@ -0,0 +1,2 @@
+Total	Processed 629464762 	Failed 42 traces
+

t/data/autoqc/25810_2.bam.filter.stats

@@ -0,0 +1,2 @@
+Total	Processed 649612652 	Failed 1024 traces
+

t/data/autoqc/25810_4.bam.filter.stats

@@ -0,0 +1,2 @@
+Total	Processed 653495042 	Failed 115390 traces
+