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Commit d2aabe1e authored by Robert Bossy's avatar Robert Bossy
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reject ambiguous name categories

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rewrite-taxonomy.snakefile
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......@@ -44,7 +44,7 @@ rule taxaid_full:
config['OUTDIR'] + '/' + config['DSMZ_MATCH_DIR']
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}'''
'''{config[REWRITE_TAXONOMY]} -namesFile {config[OUTDIR]}/{config[NCBI_DIR]}/names.dmp -namesFile {input}/dsmz-names.dmp -prefix ncbi: -rejectionFile reject.txt -rejectNameType in-part -rejectNameType Includes -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:
......@@ -55,4 +55,4 @@ rule taxid_full:
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}'''
'''{config[REWRITE_TAXONOMY]} -taxaDict -namesFile {config[OUTDIR]}/{config[NCBI_DIR]}/names.dmp -namesFile {input}/dsmz-names.dmp -prefix ncbi: -rejectionFile reject.txt -rejectNameType in-part -rejectNameType Includes -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}'''
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