Finishing adding NCBIfam-AMR

ebi-pf-team · Sep 9, 2024 · d1e062c · d1e062c
1 parent ffe5b0f
commit d1e062c
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Showing 2 changed files with 12 additions and 7 deletions.
diff --git a/core/jms-implementation/src/main/resources/spring/jobs/jobNCBIfamAMR-context.xml b/core/jms-implementation/src/main/resources/spring/jobs/jobNCBIfamAMR-context.xml
@@ -49,23 +49,24 @@
           class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
           parent="abstractNCBIfamAMRStep">
         <property name="dependsUpon" ref="stepNCBIfamAMRRunHmmer3"/>
-        <property name="stepDescription" value="Delete the fasta file following successful run of FPS"/>
+        <property name="stepDescription" value="Delete the fasta file following successful run of hmmsearch"/>
         <property name="fileNameTemplate" ref="fastaFileNameTemplate"/>
     </bean>
 
     <bean id="stepNCBIfamAMRStoreRawMatches"
           class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer3.NCBIfamParseStep"
           parent="abstractNCBIfamAMRStep">
         <property name="dependsUpon" ref="stepNCBIfamAMRRunHmmer3"/>
-        <property name="stepDescription" value="Parse the NCBIfam binary output and store as Filtered matches."/>
-        <property name="serialGroup" value="PARSE_NCBIFAM"/>
+        <property name="stepDescription" value="Parse the NCBIfam-AMR binary output and store as Filtered matches."/>
+        <property name="serialGroup" value="PARSE_NCBIFAM_AMR"/>
         <property name="parser">
             <bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Hmmer3MatchParser">
                 <property name="useHmmsearch" value="true"/>
                 <property name="parserSupport">
                     <bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.NCBIfamParserSupport">
-                        <property name="signatureLibraryRelease" ref="ncbifamSignatureLibraryReleaseVersion"/>
+                        <property name="signatureLibraryRelease" ref="ncbifamAMRSignatureLibraryReleaseVersion"/>
                         <property name="hmmKey" value="ACCESSION"/>
+                        <property name="isAMR" value="true"/>
                     </bean>
                 </property>
             </bean>
@@ -97,7 +98,7 @@
         </property>
         <property name="serialGroup" value="HMMER3_POST_PROCESSING"/>
         <property name="rawMatchDAO" ref="ncbifamAMRRawMatchDAO"/>
-        <property name="signatureLibrary" value="NCBIFAM"/>
+        <property name="signatureLibrary" value="NCBIFAM_AMR"/>
         <property name="filter">
             <bean class="uk.ac.ebi.interpro.scan.business.filter.AllPassRawMatchFilter"/>
         </property>
@@ -109,7 +110,11 @@
     </bean>
 
     <bean id="signatureLibraryReleaseNcbifamAMR" class="uk.ac.ebi.interpro.scan.model.SignatureLibraryRelease">
-        <constructor-arg type="uk.ac.ebi.interpro.scan.model.SignatureLibrary" value="NCBIFAM"/>
+        <constructor-arg type="uk.ac.ebi.interpro.scan.model.SignatureLibrary" value="NCBIFAM_AMR"/>
         <constructor-arg type="java.lang.String" value="${ncbifam-amr.signature.library.release}"/>
     </bean>
+
+    <bean id="ncbifamAMRSignatureLibraryReleaseVersion" class="java.lang.String">
+        <constructor-arg value="${ncbifam-amr.signature.library.release}"/>
+    </bean>
 </beans>
diff --git a/core/model/src/main/java/uk/ac/ebi/interpro/scan/model/SignatureLibrary.java b/core/model/src/main/java/uk/ac/ebi/interpro/scan/model/SignatureLibrary.java
@@ -35,7 +35,7 @@ public enum SignatureLibrary {
     HAMAP("Hamap", "Description to be added", true),
     MOBIDB_LITE("MobiDBLite", "Predicts disordered protein regions", false),
     NCBIFAM("NCBIfam", "NCBIfam is a collection of protein families based on Hidden Markov Models (HMMs)", true),
-    NCBIFAM_AMR("NCBIfam", "NCBIfam-AMR is a collection of Hidden Markov Models (HMMs) used for the detection of antimicrobial resistance genes", true),
+    NCBIFAM_AMR("NCBIfam-AMR", "NCBIfam-AMR is a collection of Hidden Markov Models (HMMs) used for the detection of antimicrobial resistance genes", true),
     PANTHER("PANTHER", "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.", true),
     PFAM("Pfam", "Description to be added", true),
     PHOBIUS("Phobius", "Prediction of signal peptides and trans-membrane regions", false),