... | @@ -13,76 +13,3 @@ The solution is to navigate to the folder `.../ete3/ncbi_taxonomy/SQLite-Levensh |
... | @@ -13,76 +13,3 @@ The solution is to navigate to the folder `.../ete3/ncbi_taxonomy/SQLite-Levensh |
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Reference : https://github.com/etetoolkit/ete/issues/173
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Reference : https://github.com/etetoolkit/ete/issues/173
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## Usage
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First time loading the taxdump
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```
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mkbdr validate --fasta resources/test/raw.fasta \
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--ncbi_taxdump "TAXO/taxdump_2021.tar.gz" \
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--output_prefix "test_raw"
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```
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taxdump previously loaded (faster)
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```
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mkbdr validate --fasta resources/test/raw.fasta \
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--output_prefix "test_raw"
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```
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Apply curation
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```
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mkbdr validate --fasta resources/test/raw.fasta \
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--curate curated_taxon.csv
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--output_prefix "test_curated"
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```
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Generate a curation csv file
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```
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mkbdr curegen --fasta test_raw_faulty_taxon.fasta \
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--output_prefix "test"
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```
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Specify the globalnames database to query
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```
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mkbdr curegen --fasta test_raw_faulty_taxon.fasta \
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--output_prefix "test" \
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--database_globalnames 'Catalogue of Life'
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```
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_______________________________________________________________________________
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crash test
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```
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python3 mkbdr validate --fasta teleo_ok.fasta --curate curated_taxon.csv --output_prefix "truc"
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cd TAXO/testouille; tar zxvf taxdump_2021.tar.gz ; cd ../../
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python3 mkbdr validate --fasta teleo_ok.fasta --curate curated_taxon.csv --output_prefix "truc" --curate curated_taxon.csv --ncbi_taxdump TAXO/testouille --ncbi_taxdump_edition
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```
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mkbdr validate --fasta teleo_ok.fasta --curate curated_taxon.csv --output_prefix "laetinicer" --ncbi_taxdump_edition --ncbi_taxdump TAXO/testouille
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obitools
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```
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conda activate obitools
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ecotag -t TAXO/testouille -R truc_valide.fasta -m 0.95 -r nimp.fasta
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```
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```
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### Taxdump Files
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wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
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tar zxvf taxdump.tar/gz
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cd TAXO/testouille; tar zxvf taxdump_2021.tar.gz ; cd ../../
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