obiaddtaxids1

Description of obiaddtaxids the obiaddtaxids command annotates sequence records with a taxid based on a taxon scientific name stored in the sequence record header. taxonomic information linking a taxid to a taxon scientific name is stored in a database formatted as an ecopcr database (see obitaxonomy) or a ncbi taxdump (see ncbi ftp site). the way to extract the taxon scientific name from the sequence record header can be specified by two options: for each sequence record, obiaddtaxids tries to match the extracted taxon scientific name with those stored in the taxonomic database. otherwise,

Options

-f <FORMAT>, --format=<FORMAT>

Format of the sequence file. Possible formats are:

•: raw: for regular OBITools extended fasta files (default value).

•: UNITE: for fasta files downloaded from the UNITE web site.

•: SILVA: for fasta files downloaded from the SILVA web site.

-k <KEY>, --key-name=<KEY>: Key of the attribute containing the taxon name in sequence files in the OBITools extended fasta format.

-a <ANCESTOR>, --restricting_ancestor=<ANCESTOR>

Enables to restrict the search of taxids under a specified ancestor.

<ANCESTOR> can be a taxid (integer) or a key (string).

•: If it is a taxid, this taxid is used to restrict the search for all the sequence records.

•: If it is a key, obiaddtaxids looks for the ancestor taxid in the corresponding attribute. This allows having a different ancestor restriction for each sequence record.

-g <FILENAME>, --genus_found=<FILENAME>

File used to store sequences with a match found for the genus.

CAUTION:

this option is not valid with the UNITE format.

-u <FILENAME>, --unidentified=<FILENAME>: File used to store sequences with no taxonomic match found.

Options

-d <FILENAME>, --database=<FILENAME>: ecoPCR taxonomy Database name

-t <FILENAME>, --taxonomy-dump=<FILENAME>: NCBI Taxonomy dump repository name

Options

-h, --help: Shows this help message and exits.

--DEBUG: Sets logging in debug mode.

Obiaddtaxids added sequence attribute

•: taxid