select taxa by id list or by id path

rewrite-taxonomy.snakefile

@@ -9,7 +9,8 @@ rule all:
         config['OUTDIR'] + '/taxa+id_microorganisms.trie',
         config['OUTDIR'] + '/taxid_full.txt',
         config['OUTDIR'] + '/taxa+id_full.txt',
-        config['OUTDIR'] + '/taxa+id_full.trie'
+        config['OUTDIR'] + '/taxa+id_full.trie',
+        config['OUTDIR'] + '/microorganisms-roots-paths.txt'
 
 
 rule check:
@@ -24,6 +25,17 @@ rule check:
         '''{config[ALVISNLP]} -J-Xmx24G -alias taxo {input} -alias trie {output} compile-taxonomy.plan'''
 
 
+rule root_paths:
+    output:
+        config['OUTDIR'] + '/microorganisms-roots-paths.txt'
+
+    input:
+        'microorganisms-roots.txt'
+
+    shell:
+        '''cut -f 5 {input} | sed -e '1d' -e '/^$/d' -e 's,$,/,' >{output}'''
+
+
 rule microorganisms:
     output:
         config['OUTDIR'] + '/{p}_microorganisms.txt'

select-taxa.plan

 <alvisnlp-plan id="select-taxa">
 
   <param name="list">
-    <alias module="taxids" param="mappingFile"/>
+    <alias module="tag.taxids" param="mappingFile"/>
+    <alias module="tag.taxroots" param="mappingFile"/>
   </param>
 
   <param name="name">
     <alias module="name" param="featureValue"/>
-    <alias module="overlaps" param="layerName"/>
+  </param>
+
+  <param name="column">
+   <alias module="tag.taxids" param="keyColumn"/>
+   <alias module="tag.taxroots" param="keyColumn"/>
+  </param>
+
+  <param name="mode">
+    <alias module="tag" param="select"/>
   </param>
 
   <name class="SetFeature">
@@ -14,12 +23,23 @@
     <featureName>select-taxa-name</featureName>
   </name>
 
-  <taxids class="FileMapper">
-    <target>documents.sections.layer:taxa</target>
-    <form>@taxid</form>
-    <targetFeatures>selected-taxa</targetFeatures>
-  </taxids>
-    
+  <tag>
+    <select>taxids</select>
+
+    <taxids class="FileMapper">
+      <target>documents.sections.layer:taxa</target>
+      <form>@taxid</form>
+      <targetFeatures>selected-taxa</targetFeatures>
+    </taxids>
+
+    <taxroots class="FileMapper">
+      <target>documents.sections.layer:taxa</target>
+      <form>@path ^ "/"</form>
+      <operator>prefix</operator>
+      <targetFeatures>selected-taxa</targetFeatures>
+    </taxroots>
+  </tag>
+  
   <layer class="Action">
     <target>documents.sections.layer:taxa[@selected-taxa]</target>
     <action>
@@ -30,6 +50,4 @@
     <addToLayer/>
     <setFeatures/>
   </layer>
-
-  <ovrelaps class="RemoveOverlaps"/>
 </alvisnlp-plan>

test.plan

@@ -9,8 +9,14 @@
     <compiledDict>output/taxa+id_full.trie</compiledDict>
   </ner-taxa>
 
-  <select-microorganisms href="select-taxa.plan">
+  <select-microorganisms-taxids href="select-taxa.plan">
     <list>output/taxid_microorganisms.txt</list>
-    <name>microorganisms</name>
-  </select-microorganisms>
+    <name>microorganisms-taxids</name>
+  </select-microorganisms-taxids>
+
+  <select-microorganisms-taxroots href="select-taxa.plan">
+    <list>output/microorganisms-roots-paths.txt</list>
+    <name>microorganisms-taxroots</name>
+    <mode>taxroots</mode>
+  </select-microorganisms-taxroots>
 </alvisnlp-plan>