Commit 77fd269a authored by peguerin's avatar peguerin
Browse files

readme update

parent 6dd2da6c
......@@ -56,100 +56,3 @@ For further information or help, don't hesitate to get in touch on Slack (you ca
## Environment
To create environments with required softwares:
```
conda env create -f envs/obitools_envs.yaml
conda env create -f envs/pylib_cbdr.yaml
```
* Obitools
```
conda activate obitools
```
* Required python libraries to build custom reference database
```
conda activate pylib_cbdr
```
## 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 ../../
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