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.. automodule:: obiselect
In each group as definied by a set of `-c` options, sequence records are ordered according
to a score function. The `N` first sequences (`N`is selected using the `-n` option) are kept
in the result subset of sequence records.
By default the score function is a random function and one sequence record is retrieved per
group. This leads to select randomly one sequence per group.
:py:mod:`obiselect` specific options
------------------------------------
.. cmdoption:: -c <KEY>, --category-attribute=<KEY>
Attribute used to categorize the sequence records. Several ``-c`` options can be combined.
.. TIP:: The ``<KEY>`` can be simply the key of an attribute, or a *Python* expression
similarly to the ``-p`` option of :py:mod:`obigrep`.
*Example:*
.. code-block:: bash
> obiselect -c sample -c seq_length seq.fasta
This command select randomly one sequence record per sample and sequence length from
the sequence records included in the `seq.fasta` file.
The selected sequence records are printed on the screen.
.. cmdoption:: -n <INTEGER>, --number=<INTEGER>
Indicates how many sequence records per group have to be retrieved.
If the size of the group is lesser than this `NUMBER`, the whole group
is retrieved.
*Example:*
.. code-block:: bash
> obiselect -n 2 -c sample -c seq_length seq.fasta
This command has the same effect than the previous example except that two
sequences are retrieved by class of sample/length.
.. cmdoption:: --merge=<KEY>
Attribute to merge.
*Example:*
.. code-block:: bash
> obiselect -c seq_length -n 2 -m sample seq1.fasta > seq2.fasta
This command keeps two sequences per sequence length, and records how
many times they were observed for each sample in the new attribute
``merged_sample``.
.. cmdoption:: --merge-ids
Adds a ``merged`` attribute containing the list of sequence record ids merged
within this group.
.. cmdoption:: -m, --min
Sets the function used for scoring sequence records into a group to the minimum function.
The minimum function is applied to the values used to define categories (see option `-c`).
Sequences will be ordered according to the distance of their values to the minimum value.
.. cmdoption:: -M, --max
Sets the function used for scoring sequence records into a group to the maximum function.
The maximum function is applied to the values used to define categories (see option `-c`).
Sequences will be ordered according to the distance of their values to the maximum value.
.. cmdoption:: -a, --mean
Sets the function used for scoring sequence records into a group to the mean function.
The mean function is applied to the values used to define categories (see option `-c`).
Sequences will be ordered according to the distance of their values to the mean value.
.. cmdoption:: --median
Sets the function used for scoring sequence records into a group to the median function.
The median function is applied to the values used to define categories (see option `-c`).
Sequences will be ordered according to the distance of their values to the median value.
.. cmdoption:: -f FUNCTION, --function=FUNCTION
Sets the function used for scoring sequence records into a group to a user define function.
The user define function is declared using `Python` syntax. Attribute keys can be used as variables.
An extra `sequence` variable representing the full sequence record is available. If option for
loading a taxonomy database is provided, a `taxonomy` variable is also available.
The function is estimated for each sequence record and the minimum value of this function in
each group.
Sequences will be ordered in each group according to the distance of their function estimation
to the minimum value of their group.
.. include:: ../optionsSet/inputformat.txt
.. include:: ../optionsSet/taxonomyDB.txt
.. include:: ../optionsSet/outputformat.txt
.. include:: ../optionsSet/defaultoptions.txt
:py:mod:`obiselect` added sequence attributes
---------------------------------------------
- :doc:`class <../attributes/class>`
- :doc:`distance <../attributes/distance>`
- :doc:`merged <../attributes/merged>`
- :doc:`class <../attributes/class>`
- :doc:`merged_* <../attributes/merged_star>`
- :doc:`select <../attributes/select>`
:py:mod:`obiselect` used sequence attribute
-------------------------------------------
- :doc:`taxid <../attributes/taxid>`
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