fixed bug some entries contain tab character, added check step

.gitignore

-taxa+id_microorganisms.txt
 _attic/
 output/
 .snakemake/

check-taxonomy.plan

+<alvisnlp-plan id="check-taxonomy">
+  <param name="taxo">
+    <alias module="read-taxonomy" param="dictFile"/>
+  </param>
+  
+  <param name="finish">
+    <alias module="finish" param="corpusFile"/>
+  </param>
+  
+  <read-taxonomy class="TabularProjector">
+    <targetLayerName>__dummy</targetLayerName>
+    <valueFeatures>,taxid,canonical-name,path,pos,rank,species-taxid,species-name</valueFeatures>
+  </read-taxonomy>
+
+  <finish class="TabularExport">
+    <outDir>.</outDir>
+    <lines>$</lines>
+    <columns>"checked"</columns>
+  </finish>
+</alvisnlp-plan>

dsmz-match.py

@@ -77,7 +77,7 @@ class BacDiveEntry:
         for sne in self.root.iterfind('./strain_availability/strains/list-item/strain_number'):
             if sne.text is None:
                 continue
-            yield from (snt.strip() for snt in re.split('[,\n]', sne.text))
+            yield from (' '.join(snt.strip().split()) for snt in re.split('[,\n]', sne.text))
         desig = self.root.findtext('./taxonomy_name/strains/list-item/designation')
         if desig is not None and desig != '':
             for d in re.split('[,;]', desig):

rewrite-taxonomy.snakefile

 configfile: 'config.yaml'
 
+
+rule check:
+    input:
+        config['OUTDIR'] + '/taxa+id_microorganisms.txt'
+
+    output:
+        config['OUTDIR'] + '/finish.txt'
+
+
+    shell:
+        '''{config[ALVISNLP]} -J-Xmx12G -alias taxo {input} -alias finish {output} check-taxonomy.plan'''
+
+
 rule microorganisms:
     output:
         config['OUTDIR'] + '/taxa+id_microorganisms.txt'