Curegen.md

@@ -18,4 +18,68 @@ This table summarizes the command-line arguments which are using by `mkbdr cureg
 | `--ncbi_taxdump_load` | `-l` | FALSE | load NCBI taxonomy from NCBI taxonomy folder path |
 
 
+# Example of commands
+
+### The simplest case:
+
+
+This command read `res_faulty_taxon.fasta` previously generated by `mkbdr validate` and generate a curation CSV file called `mycure.csv`.
+
+```
+mkbdr curegen --fasta res_faulty_taxon.fasta --output_prefix "mycure"
+```
+
+
+### Select a prefered database for geonames:
+
+By default MKBDR seeks synonyms of genus and family names in 'Fishbase' database usinge geonames. It is possible to specify another database such as 'Catalog of Life' with the argument `--database_globalnames`.
+
+```
+mkbdr curegen --fasta test_raw_faulty_taxon.fasta \
+--output_prefix "cure" \
+--database_globalnames 'Catalogue of Life'
+```
+
+### Using local NCBI taxonomy files
+
+It is possible to load local NCBI taxonomy files. Here we load `path/to/ncbi_taxo` with arguments `--ncbi_taxdump` and `--ncbi_taxdump_load`.
+
+```
+mkbdr curegen --fasta test_raw_faulty_taxon.fasta \
+--output_prefix "cure" \
+--ncbi_taxdump path/to/ncbi_taxo \
+--ncbi_taxdump_load
+```
+
+## Outputs
+
+The **curegen** module generates a curation CSV file. (see Files definition section for more information). The curation file is a `;`-separated CSV file. It is a matrix with records (taxonomy) as row and the following columns:
+
+* `current_name` is the species name of the record in the input FASTA file
+* `ncbi_name`is the curated species name of the record
+* `genus` is the curated genus name of the record
+* `family` is the curated family name of the record
+* `ncbi_rank` is the NCBI knowledge level of curated names (species, genus or family)
+* `method` gives non-mandatory information about the source of the curation of the record (i.e. geonames or NCBI synonyms seeking)
+
+
+Let's see an example of result returned by curegen:
+
+
+| current_name | ncbi_name | genus | family | ncbi_rank | method |
+|---|---|---|---|---|---|
+| Albula forsteri | Albula argentea | Albula | Albulidae | species | NCBI synonym score=1.0 |
+| Hyporhamphus melanopterus | NA | Hyporhamphus | Hemiramphidae | genus | Catalogue of Life |
+
+
+
+* A NCBI synonym has been found for _Albula forsteri_ species name. This is _Albula argentea_.
+* A Catalog of Life matching with NCBI has been found for _Hyporhamphus_ at genus level.
+
+
+
+The curation CSV file can be used with `mkbdr validate --curate` command to perform curation on faulty taxonomy records.
+
+:warning: This file is a raw product and need to be manually checked before to be used as input of `mkbdr validate --curate` to perform curation of species name and local taxonomy.
+