aligned_coords checked before being added to FASTA headers

pfam_hash keys checked before being used
eead-csic-compbio · Sep 10, 2018 · 2e449ad · 2e449ad
1 parent c17c8c4
commit 2e449ad
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Showing 3 changed files with 16 additions and 8 deletions.
diff --git a/CHANGES.txt b/CHANGES.txt
@@ -267,3 +267,5 @@
 28082018: bug fixed: get_homologues-pl -X now removes previous DIAMOND results of one vs others when new genomes are added (thanks alexweisberg)
 03092018: added section 'Output files explained' to EST manual (thanks Lior Glick)
 05092018: updated shebangs of some scripts and added use warnings instead of -w (thanks morgansobol)
+10092018: aligned_coords checked before being added to FASTA headers @ get_homologues* (use Warnings)
+10092018: pfam_hash keys checked before being used (use Warnings)
diff --git a/get_homologues-est.pl b/get_homologues-est.pl
@@ -876,7 +876,8 @@
   $proteome_size = $psize{$taxa[$taxon]};
 
   # update minimal proteome size
-  if($min_proteome_size == -1 || $proteome_size < $min_proteome_size)
+  if((defined($min_proteome_size) && $min_proteome_size== -1) || 
+    (defined($min_proteome_size) && defined($proteome_size) && $proteome_size < $min_proteome_size))
   {
     $min_proteome_size = $proteome_size;
     $smallest_proteome_name = $taxa[$taxon];
@@ -2310,7 +2311,7 @@
   # 4.3.1) print reference gene/protein
   push(@taxon_names,$gindex2[$gene]); # global set in phyTools:constructAllFasta
   $header = $sequence_data[$gene];
-  if(!$saveRAM)
+  if(!$saveRAM && defined($aligned_coords{$gene}{'first'}))
   {
     chomp($header);
     $header .= " | aligned:$aligned_coords{$gene}{'first'}-$aligned_coords{$gene}{'last'} ".
@@ -2812,11 +2813,13 @@ sub split_Pfam_clusters
     # check number of Pfam domain strings in this cluster
     my (%Pfam_strings);
 
-    $pfam = "$pfam_hash{$cluster}" || '';
+    if(defined($pfam_hash{$cluster})){ $pfam = "$pfam_hash{$cluster}" }
+    else{ $pfam = '' }
     push(@{$Pfam_strings{$pfam}},$cluster);
     foreach $orth (@{$ref_hash_orths->{$cluster}})
     {
-      $pfam = "$pfam_hash{$orth}" || '';
+      if(defined($pfam_hash{$orth})){ $pfam = "$pfam_hash{$orth}" }
+      else{ $pfam = '' }
       push(@{$Pfam_strings{$pfam}},$orth);
     } #print "<".$#{$ref_hash_orths->{$cluster}}." ".scalar(@{$ref_hash_orths->{$cluster}})."\n";
 

diff --git a/get_homologues.pl b/get_homologues.pl
@@ -1120,7 +1120,8 @@
   $proteome_size = $psize{$taxa[$taxon]};
 
   # update minimal proteome size
-  if($min_proteome_size == -1 || $proteome_size < $min_proteome_size)
+  if((defined($min_proteome_size) && $min_proteome_size== -1) || 
+    (defined($min_proteome_size) && defined($proteome_size) && $proteome_size < $min_proteome_size))
   {
     $min_proteome_size = $proteome_size;
     $smallest_proteome_name = $taxa[$taxon];
@@ -2645,7 +2646,7 @@
   # 4.3.1) print reference gene/protein
   push(@taxon_names,$gindex2[$gene]); # global set in phyTools:constructAllFasta
   $header = $sequence_data[$gene];
-  if(!$saveRAM)
+  if(!$saveRAM && defined($aligned_coords{$gene}{'first'}))
   {
     chomp($header);
     $header .= " | aligned:$aligned_coords{$gene}{'first'}-$aligned_coords{$gene}{'last'} ".
@@ -3203,11 +3204,13 @@ sub split_Pfam_clusters
     # check number of Pfam domain strings in this cluster
     my (%Pfam_strings);
 
-    $pfam = "$pfam_hash{$cluster}" || '';
+    if(defined($pfam_hash{$cluster})){ $pfam = "$pfam_hash{$cluster}" }
+    else{ $pfam = '' }
     push(@{$Pfam_strings{$pfam}},$cluster);
     foreach $orth (@{$ref_hash_orths->{$cluster}})
     {
-      $pfam = "$pfam_hash{$orth}" || '';
+      if(defined($pfam_hash{$orth})){ $pfam = "$pfam_hash{$orth}" }
+      else{ $pfam = '' }
       push(@{$Pfam_strings{$pfam}},$orth);
     } #print "<".$#{$ref_hash_orths->{$cluster}}." ".scalar(@{$ref_hash_orths->{$cluster}})."\n";