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.. automodule:: ecotag
:py:mod:`ecotag` specific options
---------------------------------
.. cmdoption:: -R <FILENAME>, --ref-database=<FILENAME>
<FILENAME> is the fasta file containing the reference sequences
.. cmdoption:: -m FLOAT, --minimum-identity=FLOAT
When the best match with the reference database present an identity
level below FLOAT, the taxonomic assignment for the sequence record
is not computed. The sequence record is nevertheless included in the
output file. FLOAT is included in a [0,1] interval.
.. cmdoption:: --minimum-circle=FLOAT
minimum identity considered for the assignment circle.
FLOAT is included in a [0,1] interval.
.. cmdoption:: -x RANK, --explain=RANK
.. cmdoption:: -u, --uniq
When this option is specified, the program first dereplicates the sequence
records to work on unique sequences only. This option greatly improves
the program's speed, especially for highly redundant datasets.
.. cmdoption:: --sort=<KEY>
The output is sorted based on the values of the relevant attribute.
.. cmdoption:: -r, --reverse
The output is sorted in reverse order (should be used with the --sort option).
(Works even if the --sort option is not set, but could not find on what
the output is sorted).
.. cmdoption:: -E FLOAT, --errors=FLOAT
FLOAT is the fraction of reference sequences that will
be ignored when looking for the lowest common ancestor. This
option is useful when a non-negligible proportion of reference sequences
is expected to be assigned to the wrong taxon, for example because of
taxonomic misidentification. FLOAT is included in a [0,1] interval.
.. cmdoption:: -M INTEGER, --min-matches=FLOAT
Define the minimum congruent assignation. If this minimum is reached and
the -E option is activated, the lowest common ancestor algorithm tolarated
that some sequences do not provide the same taxonomic annotation (see the
-E option).
.. cmdoption:: --cache-size=INTEGER
A cache for computed similarities is maintained by `ecotag`. the default
size for this cache is 1,000,000 of scores. This option allows to change
the cache size.
.. include:: ../optionsSet/taxonomyDB.txt
.. include:: ../optionsSet/inputformat.txt
.. include:: ../optionsSet/outputformat.txt
.. include:: ../optionsSet/defaultoptions.txt
:py:mod:`ecotag` added sequence attributes
------------------------------------------
.. hlist::
:columns: 3
- :doc:`best_identity <../attributes/best_identity>`
- :doc:`best_match <../attributes/best_match>`
- :doc:`family <../attributes/family>`
- :doc:`family_name <../attributes/family_name>`
- :doc:`genus <../attributes/genus>`
- :doc:`genus_name <../attributes/genus_name>`
- :doc:`id_status <../attributes/id_status>`
- :doc:`order <../attributes/order>`
- :doc:`order_name <../attributes/order_name>`
- :doc:`rank <../attributes/rank>`
- :doc:`scientific_name <../attributes/scientific_name>`
- :doc:`species <../attributes/species>`
- :doc:`species_list <../attributes/species_list>`
- :doc:`species_name <../attributes/species_name>`
- :doc:`taxid <../attributes/taxid>`
|
