Merge branch 'singlehmmer' into pfam37

core/io/src/main/java/uk/ac/ebi/interpro/scan/io/model/HmmerModelParser.java

@@ -31,8 +31,11 @@ public class HmmerModelParser extends AbstractModelFileParser {
     /**
      * Matches the name line.
      * Group 1: Model name.
+     *
+     * NOTE: SFLD NAMEs may have '\$\d+' at end of string and this will be stripped off.
+     * This numbers are used to guarantee unique names.
      */
-    private static final Pattern NAME_LINE = Pattern.compile("^NAME\\s+(.+)$");
+    private static final Pattern NAME_LINE = Pattern.compile("^NAME\\s+(.*?)(?:\\$\\d+)?$");
 
     /**
      * Matches the Description line.

core/io/src/main/java/uk/ac/ebi/interpro/scan/io/superfamily/model/SuperFamilyModelParser.java

@@ -48,8 +48,8 @@ public class SuperFamilyModelParser extends AbstractModelFileParser {
     private static final Pattern DESC_LINE = Pattern.compile("^DESC\\s+(.+)$");
 
     /**
-     * Matches the signature accession line (but needs "SSF" prefix adding) and if there is a version number it will be
-     * stripped off (but doesn't really apply here).
+     * Matches the signature accession line (but needs "SSF" prefix adding) and if there is a 'version' number it will be
+     * stripped off. 'version' numbers are used to guarantee unique SuperFamily ACCs.
      */
     private static final Pattern ACCESSION_PATTERN = Pattern.compile("^ACC\\s+([A-Z0-9]+)\\.?.*$");
 

core/jms-implementation/src/main/resources/application-default.properties

@@ -78,12 +78,9 @@ binary.hmmer2.hmmsearch.path=${bin.directory}/hmmer/hmmer2/2.3.2/hmmsearch
 binary.hmmer2.hmmpfam.path=${bin.directory}/hmmer/hmmer2/2.3.2/hmmpfam
 
 # HMMER 3
-binary.hmmer3.path=${bin.directory}/hmmer/hmmer3/3.1b1
-binary.hmmer3.hmmscan.path=${bin.directory}/hmmer/hmmer3/3.1b1/hmmscan
-binary.hmmer3.hmmsearch.path=${bin.directory}/hmmer/hmmer3/3.1b1/hmmsearch
-binary.hmmer33.path=${bin.directory}/hmmer/hmmer3/3.3
-binary.hmmer33.hmmscan.path=${bin.directory}/hmmer/hmmer3/3.3/hmmscan
-binary.hmmer33.hmmsearch.path=${bin.directory}/hmmer/hmmer3/3.3/hmmsearch
+binary.hmmer3.path=${bin.directory}/hmmer/hmmer3/3.3
+binary.hmmer3.hmmscan.path=${bin.directory}/hmmer/hmmer3/3.3/hmmscan
+binary.hmmer3.hmmsearch.path=${bin.directory}/hmmer/hmmer3/3.3/hmmsearch
 
 # Misc
 binary.getorf.path=${bin.directory}/nucleotide/getorf

core/jms-implementation/src/main/resources/spring/jobs/jobAntiFam-context.xml

@@ -39,7 +39,7 @@
         <property name="dependsUpon" ref="stepAntiFamWriteFastaFile"/>
         <property name="stepDescription" value="Run HMMER 3 Binary for selected proteins"/>
         <property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
-        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer33.hmmsearch.path}"/>
+        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
         <property name="binarySwitches" value="${hmmer3.hmmsearch.switches.antifam} ${hmmer3.hmmsearch.cpu.switch.antifam}"/>
         <property name="usesFileOutputSwitch" value="true"/>
         <property name="outputFileNameTemplate" ref="rawAnalysisOutputFileTemplate"/>

core/jms-implementation/src/main/resources/spring/jobs/jobFunFam-context.xml

@@ -36,8 +36,8 @@
           parent="abstractCathFunFamStep">
         <property name="dependsUpon" ref="stepCathFunFamWriteFasta"/>
         <property name="stepDescription" value="Run HMMER3"/>
-        <property name="fullPathToHmmScanBinary" value="${binary.hmmer33.hmmscan.path}"/>
-        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer33.hmmsearch.path}"/>
+        <property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
+        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
         <property name="binarySwitches"
                   value="${hmmer3.hmmsearch.switches.gene3d} ${hmmer3.hmmsearch.cpu.switch.gene3d}"/>
         <property name="fullPathToHmmFile" value="${gene3d.hmm.path}"/>
@@ -91,7 +91,7 @@
         <property name="usesFileOutputSwitch" value="true"/>
         <property name="outputFileNameTemplate" ref="rawAnalysisOutputThreeFileTemplate"/>
         <property name="cathResolveHitsOutputFileNameTemplate" ref="rawAnalysisOutputFourFileTemplate"/>
-        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer33.hmmsearch.path}"/>
+        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
         <property name="hmmsearchBinarySwitches" value="${hmmer3.hmmsearch.switches.funfam} ${hmmer3.hmmsearch.cpu.switch.funfam}"/>
         <property name="fullPathToCathResolveBinary" value="${cath.resolve.hits.path}"/>
         <property name="cathResolveBinarySwitches" value="${cath.resolve.hits.switches.funfam}"/>

core/jms-implementation/src/main/resources/spring/jobs/jobGene3d-context.xml

@@ -36,8 +36,8 @@
           parent="abstractCathGene3dStep">
         <property name="dependsUpon" ref="stepCathGene3dWriteFasta"/>
         <property name="stepDescription" value="Run HMMER3"/>
-        <property name="fullPathToHmmScanBinary" value="${binary.hmmer33.hmmscan.path}"/>
-        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer33.hmmsearch.path}"/>
+        <property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
+        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
         <property name="binarySwitches"
                   value="${hmmer3.hmmsearch.switches.gene3d} ${hmmer3.hmmsearch.cpu.switch.gene3d}"/>
         <property name="fullPathToHmmFile" value="${gene3d.hmm.path}"/>

core/jms-implementation/src/main/resources/spring/jobs/jobHAMAP-context.xml

@@ -39,8 +39,8 @@
           parent="abstractHamapHMMStep">
         <property name="dependsUpon" ref="stepHamapHMMWriteFastaFile"/>
         <property name="stepDescription" value="Run HMMER3"/>
-        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer33.hmmsearch.path}"/>
-        <property name="fullPathToHmmScanBinary" value="${binary.hmmer33.hmmscan.path}"/>
+        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
+        <property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
         <property name="singleSeqMode" value="false"/>
         <property name="binarySwitches" value="${hmmer3.hmmsearch.switches.hmmfilter} ${hmmer3.hmmsearch.cpu.switch.hmmfilter}"/>
         <property name="fullPathToHmmFile" value="${hamap.hmm.path}"/>

core/jms-implementation/src/main/resources/spring/jobs/jobNCBIfam-context.xml

@@ -38,7 +38,7 @@
         <property name="dependsUpon" ref="stepNCBIfamWriteFastaFile"/>
         <property name="stepDescription" value="Run fingerprintscan Binary for selected proteins"/>
         <property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
-        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer33.hmmsearch.path}"/>
+        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
         <property name="binarySwitches" value="${hmmer3.hmmsearch.switches.ncbifam} ${hmmer3.hmmsearch.cpu.switch.ncbifam}"/>
         <property name="usesFileOutputSwitch" value="true"/>
         <property name="outputFileNameTemplate" ref="rawAnalysisOutputFileTemplate"/>

core/jms-implementation/src/main/resources/spring/jobs/jobPIRSF-context.xml

@@ -41,8 +41,8 @@
         <property name="dependsUpon" ref="stepPIRSFWriteFasta"/>
         <property name="stepDescription" value="Run hmmer3 Binary for selected proteins"/>
         <property name="forceHmmsearch" value="${pirsf.hmmsearch.force}"/>
-        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer33.hmmsearch.path}"/>
-        <property name="fullPathToHmmScanBinary" value="${binary.hmmer33.hmmscan.path}"/>
+        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
+        <property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
         <property name="binarySwitches" value="${hmmer3.hmmsearch.switches.pirsf} ${hmmer3.hmmsearch.cpu.switch.pirsf}"/>
         <property name="fullPathToHmmFile" value="${pirsf.sfhmm.path}"/>
         <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
@@ -69,7 +69,7 @@
         <!--More specific properties-->
         <property name="perlCommand" value="${perl.command}"/>
         <property name="scriptPath" value="${binary.pirsf.pl.path}"/>
-        <property name="hmmerPath" value="${binary.hmmer33.path}"/>
+        <property name="hmmerPath" value="${binary.hmmer3.path}"/>
         <property name="sfHmmAllPath" value="${pirsf.sfhmm.path}"/>
         <property name="pirsfDatPath" value="${pirsf.dat.path}"/>
         <property name="binarySwitches" value="${pirsf.pl.binary.switches} ${pirsf.pl.binary.cpu.switch}"/>

core/jms-implementation/src/main/resources/spring/jobs/jobPanther-context.xml

@@ -61,8 +61,8 @@
         <property name="dependsUpon" ref="stepPantherWriteFastaFile"/>
         <property name="stepDescription" value="Run HMMER 3 Binary for selected proteins"/>
         <property name="forceHmmsearch" value="${panther.hmmsearch.force}"/>
-        <property name="fullPathToHmmScanBinary" value="${binary.hmmer33.hmmscan.path}"/>
-        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer33.hmmsearch.path}"/>
+        <property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
+        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
         <property name="binarySwitches" value="${hmmer3.hmmsearch.switches.panther} ${hmmer3.hmmsearch.cpu.switch.panther}"/>
         <property name="fullPathToHmmFile" value="${panther.hmm.path}"/>
         <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>

core/jms-implementation/src/main/resources/spring/jobs/jobPfam-context.xml

@@ -40,8 +40,8 @@
           parent="abstractPfamStep">
         <property name="dependsUpon" ref="stepPfamWriteFastaFile"/>
         <property name="stepDescription" value="Run HMMER 3 Binary for selected proteins"/>
-        <property name="fullPathToHmmScanBinary" value="${binary.hmmer33.hmmscan.path}"/>
-        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer33.hmmsearch.path}"/>
+        <property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
+        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
         <property name="binarySwitches" value="${hmmer3.hmmsearch.switches.pfama} ${hmmer3.hmmsearch.cpu.switch.pfama}"/>
         <property name="fullPathToHmmFile" value="${pfam-a.hmm.path}"/>
         <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>

core/jms-implementation/src/main/resources/spring/jobs/jobSFLD-context.xml

@@ -48,8 +48,8 @@
         <property name="dependsUpon" ref="stepSFLDWriteFastaFile"/>
         <property name="stepDescription" value="Run hmmer3 Binary for selected proteins"/>
         <property name="forceHmmsearch" value="${sfld.hmmsearch.force}"/>
-        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer33.hmmsearch.path}"/>
-        <property name="fullPathToHmmScanBinary" value="${binary.hmmer33.hmmscan.path}"/>
+        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
+        <property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
         <property name="binarySwitches" value="${hmmer3.hmmsearch.switches.sfld} ${hmmer3.hmmsearch.cpu.switch.sfld}"/>
         <property name="fullPathToHmmFile" value="${sfld.hmm.path}"/>
         <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>

core/jms-implementation/src/main/resources/spring/jobs/jobSuperFamily-context.xml

@@ -42,7 +42,7 @@
         -->
         <property name="dependsUpon" ref="stepSuperFamilyWriteFastaFile"/>
         <property name="stepDescription" value="Run HMMER3"/>
-        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer33.hmmscan.path}"/>
+        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmscan.path}"/>
         <property name="binarySwitches" value="${hmmer3.hmmsearch.switches.superfamily} ${hmmer3.hmmsearch.cpu.switch.superfamily}"/>
         <property name="fullPathToHmmFile" value="${superfamily.hmm.path}"/>
         <property name="usesFileOutputSwitch" value="true"/>

core/jms-implementation/support-mini-x86-32/interproscan.properties

@@ -14,8 +14,7 @@ perl.command=perl
 python3.command=python3
 
 # Binary file locations (required for setup.py)
-binary.hmmer3.path=${bin.directory}/hmmer/hmmer3/3.1b1
-binary.hmmer33.path=${bin.directory}/hmmer/hmmer3/3.3
+binary.hmmer3.path=${bin.directory}/hmmer/hmmer3/3.3
 
 ####################################
 # Member databases HMMs

core/jms-implementation/support-mini-x86-32/setup.py

@@ -80,10 +80,7 @@ def main():
     ignore = {"binary.tmhmm.path", "funfam.hmm.path", "smart.hmm.path"}
     for key, path in properties.items():
         if "hmm.path" in key and key not in ignore:
-            if key.startswith(("sfld", "superfamily")):
-                bin_key = "binary.hmmer3.path"
-            else:
-                bin_key = "binary.hmmer33.path"
+            bin_key = "binary.hmmer3.path"
 
             if os.path.isfile(path):
                 hmmfiles = [path]