Scroll to navigation

ECODBTAXSTAT(1) OBITools ECODBTAXSTAT(1)

NAME

ecodbtaxstat - description of ecodbtaxstat

The ecodbtaxstat command requires an ecopcr database and a taxonomic rank (specified by the --rank option, default species). The command outputs first the total number of sequence records in the database having taxonomic information at this rank, and then the number of sequence records for each value of this rank.

ECODBTAXSTAT SPECIFIC OPTION

--rank=<TAXONOMIC_RANK>
The taxonomic rank at which frequencies have to be computed. Possible values are:
  • class
  • family
  • forma
  • genus
  • infraclass
  • infraorder
  • kingdom
  • order
  • parvorder
  • phylum
  • species (default)
  • species group
  • species subgroup
  • subclass
  • subfamily
  • subgenus
  • subkingdom
  • suborder
  • subphylum
  • subspecies
  • subtribe
  • superclass
  • superfamily
  • superkingdom
  • superorder
  • superphylum
  • tribe
  • varietas




TAXONOMY RELATED OPTIONS

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

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

--require-rank=<RANK_NAME>
select sequence with taxid tag containing a parent of rank <RANK_NAME>

-r <TAXID>, --required=<TAXID>
required taxid

-i <TAXID>, --ignore=<TAXID>
ignored taxid

ECODBTAXSTAT USED SEQUENCE ATTRIBUTES

•
taxid



AUTHOR

The OBITools Development Team - LECA

COPYRIGHT

2019 - 2015, OBITool Development Team
January 28, 2019 1.02 12