temp fix for #17

geneontology · Apr 21, 2018 · ab071b3 · ab071b3
1 parent 238b909
commit ab071b3
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Showing 2 changed files with 13 additions and 1 deletion.
diff --git a/Makefile b/Makefile
@@ -47,7 +47,7 @@ foo:
 include Makefile-gafs
 
 neo.owl: neo.obo
-	owltools $< -o $@
+	owltools $< -o $@.tmp && ./bin/fix-obo-uris.pl $@.tmp > $@.tmp2 && mv $@.tmp2 $@
 
 Makefile-gafs: datasets.json
 	./build-neo-makefile.py -i $< > $@.tmp && mv $@.tmp $@

diff --git a/bin/fix-obo-uris.pl b/bin/fix-obo-uris.pl
@@ -0,0 +1,12 @@
+#!/usr/bin/perl -np
+s@http://purl.obolibrary.org/obo/(dictyBase|ZFIN|FB|WB|SGD|PomBase|RGD|MGI|XenBase|UniProtKB|TAIR:\s+)_@"http://identifiers.org/".fix($1)."/"@eg;
+
+sub fix {
+    $s = lc($_[0]);
+    $s =~ s@^fb$@flybase@;
+    $s =~ s@^wb$@wormbase@;
+    $s =~ s@^uniprotkb$@uniprot@;
+    $s =~ s@^tair:@tair.@;
+    return $s;
+}
+