obitaxonomy1

Adds a new taxon to the taxonomy. The new taxon is described by three values separated by colons: its scientific name, its taxonomic rank, and the taxid of its first ancestor.

> obitaxonomy -d my_ecopcr_database \
  -a 'Gentiana alpina':'species':49934

Adds a taxon with the scientific name Gentiana alpina and the rank species under the taxon whose taxid is 49934.

Minimum taxid for the newly added taxid(s).

> obitaxonomy -d my_ecopcr_database -m 1000000000 \
  -a 'Gentiana alpina':'species':49934

Adds a taxon with the scientific name Gentiana alpina and the rank species under the taxon whose taxid is 49934, with a taxid greater than or equal to 1000000000.

Deletes the local taxon with the taxid <TAXID> from the taxonomic database.

> obitaxonomy -d my_ecopcr_database -D 10000832

Deletes the local taxon with the taxid 10000832 from the taxonomic database.

Adds a new species to the taxonomy. The new species is described by its scientific name. The genus of the species must already exist in the database. The species will be added under its genus.

> obitaxonomy -d my_ecopcr_database -s 'Gentiana alpina'

Adds the species with the scientific name Gentiana alpina under the genus Gentiana.

Adds a new favorite scientific name to the taxonomy. The new name is described by two values separated by a colon: the new favorite name and the taxid of the taxon.

> obitaxonomy -d my_ecopcr_database \
  -f 'Gentiana algida':50748

Adds the favorite scientific name Gentiana algida for the taxid 50748 in the taxonomic database.

Adds all the taxa from a sequence file in OBITools extended doc:fasta <../fasta> format, and eventually their ancestors to the database (see documentation). Each sequence record must contain the attribute specified by the -k option.

> obitaxonomy -d my_ecopcr_database \
  -k my_taxon_name_key -F my_sequences.fasta

Adds the taxon of each sequence record from the file my_sequences.fasta in the taxonomic database, based on the scientific name contained in the my_taxon_name_key attribute.

Works with the -F option. Can be a taxid (integer) or a key (string). If it is a taxid, this taxid is the default taxid under which the new taxon is added if none of his ancestors are specified or can be found. If it is a key, obitaxonomy looks for the ancestor taxid in the corresponding attribute, and the new taxon is systematically added under this ancestor. By default, the restricting ancestor is the root of the taxonomic tree for all the new taxa.

> obitaxonomy -d my_ecopcr_database -a 33090 \
  -k my_taxon_name_key -F my_sequences.fasta

Adds the taxon of each sequence record from the file my_sequences.fasta in the taxonomic database, based on the scientific name contained in the my_taxon_name_key attribute. If the genus of the new taxon cannot be found, the new taxon is added under the taxon whose taxid is 33090.

Works with the -F option. Key of the attribute containing the taxonomic paths of the taxa if they are in the headers of the sequence records. The value contained in this attribute must be of the form ‘Fungi, Agaricomycetes, Thelephorales, Thelephoraceae’ with the highest ancestors first and commas between ancestors.

> obitaxonomy -d my_ecopcr_database -p my_taxonomic_path_key \
  -k my_taxon_name_key -F my_sequences.fasta

Adds the taxon of each sequence record from the file my_sequences.fasta in the taxonomic database, based on the scientific name contained in the my_taxon_name_key attribute. Each ancestor contained in the my_taxonomic_path_key attribute is added if it does not already exist, and the new taxon is added under the latest ancestor of the path.