Replace references to TIGRfam with NCBIfam

WormBase · Aug 22, 2023 · 5770b05 · 5770b05
1 parent f75fa8c
commit 5770b05
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Showing 5 changed files with 6 additions and 6 deletions.
diff --git a/scripts/BLAST_scripts/dump_interpro_motif.pl b/scripts/BLAST_scripts/dump_interpro_motif.pl
@@ -72,7 +72,7 @@
 		       'blastprodom',
 		       'smart',
 		       'pfam',
-		       'tigrfam',
+		       'ncbifam',
 #		       'ncoils', # no interpro_id
 #		       'seg', # no interpro_id
 #		       'tmhmm', # no score or evalue

diff --git a/scripts/BLAST_scripts/dump_motif.pl b/scripts/BLAST_scripts/dump_motif.pl
@@ -43,7 +43,7 @@
 my $log = Log_files->make_build_log($wormbase);
 
 # define the names of the methods to be dumped
-@methods = qw(hmmpanther pfscan pirsf prints scanprosite smart tigrfam ncoils seg signalp tmhmm pfam superfamily mobidblite hamap) unless @methods;
+@methods = qw(hmmpanther pfscan pirsf prints scanprosite smart ncbifam ncoils seg signalp tmhmm pfam superfamily mobidblite hamap) unless @methods;
 
 $log->write_to("Dumping methods".@methods."\n");
 
@@ -138,7 +138,7 @@ sub now {
 	$hid = $1;
        }
        $line = "Motif_homol \"PFAM:$hid\" \"pfam\" $score $start $end $hstart $hend";
-    }elsif($meth=~/hmmpanther|pfscan|pirsf|prints|scanprosite|smart|tigrfam|superfamily/){
+    }elsif($meth=~/hmmpanther|pfscan|pirsf|prints|scanprosite|smart|ncbifam|superfamily/){
        my $prefix = uc($meth);
        my $motif = "$prefix:$hid"; # shorthand for the acedb id
        $line = "Motif_homol \"$motif\" \"$meth\" $score $start $end $hstart $hend";

diff --git a/scripts/BLAST_scripts/make_interpro.pl b/scripts/BLAST_scripts/make_interpro.pl
@@ -260,7 +260,7 @@ sub delete_results {
 
 
   # logical names in the Ensemble pipeline for the analyses used in interpro
-  my @methods = qw(scanprosite Prints pfscan blastprodom hmmpanther Smart Tigrfam Pfam PIRSF Superfamily gene3d hamap);
+  my @methods = qw(scanprosite Prints pfscan blastprodom hmmpanther Smart Ncbifam Pfam PIRSF Superfamily gene3d hamap);
 
   # get the mapping of method 2 analysis id
   my %method2analysis;

diff --git a/scripts/ENSEMBL/analysis.descriptions b/scripts/ENSEMBL/analysis.descriptions
@@ -49,7 +49,7 @@ snlRNA	small nucleolar like RNA genes
 snoRNA	small nucleolar RNA genes
 snRNA	small nuclear RNA genes
 Superfamily	PIR superfamilies as part of interpro_scan
-Tigrfam	TIGRfam HMM analysis as part of interpro_scan
+Ncbifam	NCBIfam HMM analysis as part of interpro_scan
 Tmhmm	Transmembrane domains as identified by TmHMM
 TRF	Tandem repeats identified by Tandem Repeats Finder (G. Benson, Nuc. Acids Res. 1999 27:573-580)
 tRNA	transfer RNA genes

diff --git a/scripts/ENSEMBL/lib/Domain2Interpro.pm b/scripts/ENSEMBL/lib/Domain2Interpro.pm
@@ -46,7 +46,7 @@ my %method_database = (
 		       'blastprodom' => 'PRODOM',
 		       'smart'       => 'SMART',
 		       'pfam'        => 'PFAM',
-		       'tigrfam'     => 'TIGRFAMs',
+		       'ncbifam'     => 'NCBIFAMs',
 		       'ncoils'      => 'COIL',
 		       'seg'         => 'SEG',
 		       'tmhmm'       => 'TMHMM',