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Commit 415e6022 authored by Robert Bossy's avatar Robert Bossy
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use DSMZ match result with rewrite-taxonomy

parent 53d3404d
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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}'''
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