How-to-guide.md

+
+## 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 ../../
+