Merge remote-tracking branch 'origin/pirsr2023_05' into develop

# Conflicts: # core/jms-implementation/support-mini-x86-32/work/template/interpro.zip
ebi-pf-team · Oct 25, 2023 · c52e958 · c52e958
2 parents f6b93b1 + 472e0e8
commit c52e958
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diff --git a/core/jms-implementation/src/main/resources/application-default.properties b/core/jms-implementation/src/main/resources/application-default.properties
@@ -194,11 +194,11 @@ pirsf.pl.binary.switches=--outfmt i5
 hmmer3.hmmsearch.switches.pirsf=-E 0.01 --acc
 
 # PIRSR
-pirsr.signature.library.release=2021_05
+pirsr.signature.library.release=2023_05
 pirsr.binary.path=${bin.directory}/pirsr/0.1/pirsr.py
-pirsr.srhmm.path=${data.directory}/pirsr/2021_05/sr_hmm_all
-pirsr.data.path=${data.directory}/pirsr/2021_05/
-pirsr.rules.path=${data.directory}/pirsr/2021_05/sr_uru.json
+pirsr.srhmm.path=${data.directory}/pirsr/2023_05/sr_hmm_all
+pirsr.data.path=${data.directory}/pirsr/2023_05/
+pirsr.rules.path=${data.directory}/pirsr/2023_05/sr_uru.json
 hmmer3.hmmsearch.cpu.switch.pirsr=--cpu 1
 pirsr.hmmsearch.force=true
 hmmer3.hmmsearch.switches.pirsr=-E 0.01 --acc

diff --git a/core/jms-implementation/support-mini-x86-32/bin/pirsr/0.1/PIRSR.pm b/core/jms-implementation/support-mini-x86-32/bin/pirsr/0.1/PIRSR.pm
@@ -123,7 +123,7 @@ sub process_templates {
 
 
             } else {
-                die "Failed to parse fasta block: \"$block\"\n";
+                warn ("Failed to parse fasta block: \"$block\"\n");
             }
         }
 
@@ -263,7 +263,9 @@ sub _parse_rules {
                         $group->{'label'} = $1;
                         $group->{'start'} = $2;
                         $group->{'end'} = $3;
-                        $group->{'desc'} = $5;
+                        my $desc = $5 // '';
+                        $desc =~ s/^\s+|\s+$//g;
+                        $group->{'desc'} = $desc;
 
                 } elsif ($line =~ /\AFT\s+Group\:\s+(\d+)\;\s+Condition\:\s+(.*)\z/) {
 
@@ -274,7 +276,9 @@ sub _parse_rules {
 
                 } elsif ($line =~ /\AFT\s+(.*)\z/) {
 
-                    $group->{'desc'} .= " $1";
+                    my $desc = $1 // '';
+                    $desc =~ s/^\s+|\s+$//g;
+                    $group->{'desc'} .= " $desc";
 
                 } else {
                     die "Failed to parse Group line: \"$line\"\n";
@@ -307,6 +311,12 @@ sub align_template {
 
     my $prot_id = $rule->{'Feature'}->{'from'};
 
+    if (!$prot_id) {
+        warn ("No from template available for rule $rule->{AC}.") if ($self->verbose);
+        $rule->{'ignore'} = 1;
+        return $rule;
+    }
+
     my $fasta_file = "$self->{data_folder}/sr_tp/${prot_id}.fa";
 
     open (my $in, '<', "$fasta_file") or die "Failed top open $fasta_file file: $!\n";