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.. automodule:: obiclean
:py:mod:`obiclean` specific options
-----------------------------------
.. cmdoption:: -d <INTEGER>, --distance=<INTEGER>
Maximum numbers of differences between two variant sequences (default: 1).
.. cmdoption:: -s <KEY>, --sample=<KEY>
Attribute containing sample descriptions.
.. cmdoption:: -r <FLOAT>, --ratio=<FLOAT>
Threshold ratio between counts (rare/abundant counts) of two sequence records
so that the less abundant one is a variant of the more abundant
(default: 1, i.e. all less abundant sequences are variants).
.. cmdoption:: -C, --cluster
Switch :py:mod:`obiclean` into its clustering mode. This adds information
to each sequence about the true.
.. cmdoption:: -H, --head
Select only sequences with the head status in a least one sample.
.. cmdoption:: -g, --graph
Creates a file containing the set of DAG used by the obiclean clustering algorithm.
The graph file follows the `dot` format
.. include:: ../optionsSet/inputformat.txt
.. include:: ../optionsSet/outputformat.txt
.. include:: ../optionsSet/defaultoptions.txt
:py:mod:`obiclean` used sequence attributes
-----------------------------------------------
.. hlist::
:columns: 3
- :doc:`count <../attributes/count>`
:py:mod:`obiclean` added sequence attributes
-----------------------------------------------
.. hlist::
:columns: 3
- :doc:`obiclean_cluster <../attributes/obiclean_cluster>`
- :doc:`obiclean_count <../attributes/obiclean_count>`
- :doc:`obiclean_head <../attributes/obiclean_head>`
- :doc:`obiclean_headcount <../attributes/obiclean_headcount>`
- :doc:`obiclean_internalcount <../attributes/obiclean_internalcount>`
- :doc:`obiclean_samplecount <../attributes/obiclean_samplecount>`
- :doc:`obiclean_singletoncount <../attributes/obiclean_singletoncount>`
- :doc:`obiclean_status <../attributes/obiclean_status>`
|
