ecotag.rst 3.12 KB
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.. automodule:: ecotag
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   :py:mod:`ecotag` specific options
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   ---------------------------------
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   .. cmdoption::  -R <FILENAME>, --ref-database=<FILENAME>

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        <FILENAME> is the fasta file containing the reference sequences

   .. cmdoption::  -m FLOAT, --minimum-identity=FLOAT
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        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
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        minimum identity considered for the assignment circle.
        FLOAT is included in a [0,1] interval.
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   .. cmdoption::  -x RANK, --explain=RANK
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   .. cmdoption::  -u, --uniq
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        When this option is specified, the program first dereplicates the sequence
        records to work on unique sequences only. This option greatly improves
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        the program's speed, especially for highly redundant datasets.

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   .. cmdoption::  --sort=<KEY>
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        The output is sorted based on the values of the relevant attribute.
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   .. cmdoption::  -r, --reverse
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        The output is sorted in reverse order (should be used with the --sort option).
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        (Works even if the --sort option is not set, but could not find on what
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        the output is sorted).

   .. cmdoption::  -E FLOAT, --errors=FLOAT
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        FLOAT is the fraction of reference sequences that will
        be ignored when looking for the most recent 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
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        taxonomic misidentification. FLOAT is included in a [0,1] interval.

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   .. 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.

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   .. include:: ../optionsSet/taxonomyDB.txt
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   .. include:: ../optionsSet/inputformat.txt

   .. include:: ../optionsSet/outputformat.txt

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   .. include:: ../optionsSet/defaultoptions.txt
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   :py:mod:`ecotag` added sequence attributes
   ------------------------------------------
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      .. hlist::
           :columns: 3
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           - :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>`