Running-MKBDR.md

@@ -175,9 +175,54 @@ The local taxonomy located on `customtaxonomy/` has been edited and all the faul
 * `customtaxonomy`: custom NCBI taxonomy
 
 
-## 6. Test the custom reference database
+## 6. Taxonomic assignment with our custom reference database
+
+We use our custom reference database to assign taxon with [ecotag](https://pythonhosted.org/OBITools/scripts/ecotag.html).
+
+
+* Installing ecotag with conda environment:
+
+```
+curl -LJO https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/blob/master/envs/obitools_envs.yaml
+conda env create -f envs/obitools_envs.yaml
+```
+
+Input files are:
+
+* `res_taxo_curated_valide.fasta`: fasta file containing reference sequences
+* `customtaxonomy/`: NCBI Taxonomy repository name
+* `raw.fasta`: Fasta query records file
+
+```
+conda activate obitools
+ecotag -t customtaxonomy \
+-R res_taxo_curated_valide.fasta \
+raw.fasta
+```
+
+This outputs:
+
+```
+>YCA_R0001; count=1; id_status={'res_taxo_curated_valide': True}; family=30840; species_name=Haemulon flavolineatum; best_match={'res_taxo_curated_valide': 'YCA_R0001'}; taxid_by_db={'res_taxo_curated_valide': 236585}; rank_by_db={'res_taxo_curated_valide': 'species'}; scientific_name=Haemulon flavolineatum; match_count={'res_taxo_curated_valide': 1}; rank=species; taxid=236585; species=236585; order_name=Lutjaniformes; best_identity={'res_taxo_curated_valide': 1.0}; scientific_name_by_db={'res_taxo_curated_valide': 'Haemulon flavolineatum'}; species_list={'res_taxo_curated_valide': ['Haemulon flavolineatum']}; genus_name=Haemulon; family_name=Haemulidae; genus=119374; order=2024539; species_name=Haemulon flavolineatum
+ccccaagctcaactagcaacatgcctaaaacacaaaaaatgcaaaggggaggcaagtcgt
+aa
+>YCA_R0002; count=1; id_status={'res_taxo_curated_valide': True}; family=30828; species_name=Chaetodon ocellatus; best_match={'res_taxo_curated_valide': 'YCA_R0002'}; taxid_by_db={'res_taxo_curated_valide': 466120}; rank_by_db={'res_taxo_curated_valide': 'species'}; scientific_name=Chaetodon ocellatus; match_count={'res_taxo_curated_valide': 1}; rank=species; taxid=466120; species=466120; order_name=Chaetodontiformes; best_identity={'res_taxo_curated_valide': 1.0}; scientific_name_by_db={'res_taxo_curated_valide': 'Chaetodon ocellatus'}; species_list={'res_taxo_curated_valide': ['Chaetodon ocellatus']}; genus_name=Chaetodon; family_name=Chaetodontidae; genus=37948; order=1545895; species_name=Chaetodon ocellatus
+ctccaagcctaaaactttttactttactaatgtgctgcaattgtagaggagaggcaagtc
+gtaa
+>REF-17-0642; count=1; id_status={'res_taxo_curated_valide': True}; family=54907; species_name=Albula argentea; best_match={'res_taxo_curated_valide': 'REF-17-0642;'}; taxid_by_db={'res_taxo_curated_valide': 531982}; rank_by_db={'res_taxo_curated_valide': 'species'}; scientific_name=Albula argentea; match_count={'res_taxo_curated_valide': 1}; rank=species; taxid=531982; species=531982; order_name=Albuliformes; best_identity={'res_taxo_curated_valide': 1.0}; scientific_name_by_db={'res_taxo_curated_valide': 'Albula argentea'}; species_list={'res_taxo_curated_valide': ['Albula argentea']}; genus_name=Albula; family_name=Albulidae; genus=54908; order=54906; species_name=Albula forsteri
+cctcgaattacatgagtaacaagtatataagctttaaggtagctataagaggaggtaagt
+cgtaa
+>YCA_R0449; count=1; id_status={'res_taxo_curated_valide': True}; family=30863; species_name=Stegastes xanthurus; best_match={'res_taxo_curated_valide': 'YCA_R0449;'}; taxid_by_db={'res_taxo_curated_valide': 10000000}; rank_by_db={'res_taxo_curated_valide': 'species'}; scientific_name=Stegastes xanthurus; match_count={'res_taxo_curated_valide': 1}; rank=species; taxid=10000000; species=10000000; order_name=None; best_identity={'res_taxo_curated_valide': 1.0}; scientific_name_by_db={'res_taxo_curated_valide': 'Stegastes xanthurus'}; species_list={'res_taxo_curated_valide': ['Stegastes xanthurus']}; genus_name=Stegastes; family_name=Pomacentridae; genus=80992; order=None; species_name=Stegastes xanthurus
+cccctaaatttgacatttaacaatatttaaaaccttgcacaagaaagaggggagaaaagt
+cgtaa
+```
+
+
+As we can read, all the query records have been found in our custom database including curated records such as  `REF-17-0642` with a NCBI synonym species_name=Albula argentea and `YCA_R0449` with a custom taxid=10000000.
+
+
+:seedling: We successfully made a custom reference database and tested it. 
 
-We will use