generate taxid_ files

rewrite-taxonomy.snakefile

 configfile: 'config.yaml'
 
 
+rule all:
+    input:
+        config['OUTDIR'] + '/finish.txt',
+        config['OUTDIR'] + '/taxid_microorganisms.txt'
+
+
 rule check:
     input:
         config['OUTDIR'] + '/taxa+id_microorganisms.txt'
@@ -15,17 +21,17 @@ rule check:
 
 rule microorganisms:
     output:
-        config['OUTDIR'] + '/taxa+id_microorganisms.txt'
+        config['OUTDIR'] + '/{p}_microorganisms.txt'
 
     input:
-        full=config['OUTDIR'] + '/taxa+id_full.txt',
+        full=config['OUTDIR'] + '/{p}_full.txt',
         roots='microorganisms-roots'
 
     shell:
         '''./cut-root.py {input.roots}/* <{input.full} >{output}'''
 
 
-rule full:
+rule taxaid_full:
     output:
         config['OUTDIR'] + '/taxa+id_full.txt'
 
@@ -34,3 +40,14 @@ rule full:
 
     shell:
         '''{config[REWRITE_TAXONOMY]} -namesFile {config[OUTDIR]}/{config[NCBI_DIR]}/names.dmp -namesFile {input}/dsmz-names.dmp  -prefix ncbi: -rejectionFile reject.txt -saturationFile saturate.txt -pattern '{{NAME}}\t{{TAXID}}\t{{CANONICAL}}\t{{TAXID_PATH}}\t{{POS_TAG}}\t{{RANK}}\t{{SPECIES_TAXID}}\t{{SPECIES_NAME}}\n' {config[OUTDIR]}/{config[NCBI_DIR]}/nodes.dmp {input}/dsmz-nodes.dmp >{output}'''
+
+
+rule taxid_full:
+    output:
+        config['OUTDIR'] + '/taxid_full.txt'
+
+    input:
+        config['OUTDIR'] + '/' + config['DSMZ_MATCH_DIR']
+
+    shell:
+        '''{config[REWRITE_TAXONOMY]} -taxaDict -namesFile {config[OUTDIR]}/{config[NCBI_DIR]}/names.dmp -namesFile {input}/dsmz-names.dmp  -prefix ncbi: -rejectionFile reject.txt -saturationFile saturate.txt -pattern '{{TAXID}}\t{{CANONICAL}}\t{{TAXID_PATH}}\t{{RANK}}\n' {config[OUTDIR]}/{config[NCBI_DIR]}/nodes.dmp {input}/dsmz-nodes.dmp >{output}'''