How-to-guide.md

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