diff --git a/rewrite-taxonomy.snakefile b/rewrite-taxonomy.snakefile new file mode 100644 index 0000000000000000000000000000000000000000..8ca2f6d5e8d1e9dfaf2f746bcb8e5f68f159fd51 --- /dev/null +++ b/rewrite-taxonomy.snakefile @@ -0,0 +1,11 @@ +configfile: 'config.yaml' + +rule rewrite: + output: + config['OUTDIR'] + '/taxa+id_full_with-DSMZ.txt' + + input: + config['OUTDIR'] + '/' + config['DSMZ_MATCH_DIR'] + + shell: + '''../bibliome-java-utils/test/install/bin/rewrite-taxonomy -namesFile {config[NCBI_NAMES_FILE]} -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[NCBI_NODES_FILE]} {input}/dsmz-nodes.dmp >{output}'''