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.. automodule:: obisample
:py:mod:`obisample` specific options
------------------------------------
.. cmdoption:: -s ###, --sample-size ###
Specifies the size of the generated sample.
- without the ``-a`` option, sample size is expressed as the exact number of sequence
records to be sampled (default: number of sequence records in the input file).
- with the ``-a`` option, sample size is expressed as a fraction of the
sequence record numbers in the input file
(expressed as a number between 0 and 1).
*Example:*
.. code-block:: bash
> obisample -s 1000 seq1.fasta > seq2.fasta
Samples randomly 1000 sequence records from the ``seq1.fasta`` file, with replacement,
and saves them in the ``seq2.fasta`` file.
.. cmdoption:: -a, --approx-sampling
Switches the resampling algorithm to an approximative one,
useful for large files.
The default algorithm selects exactly the number of sequence records
specified with the ``-s`` option. When the ``-a`` option is set,
each sequence record has a probability to be selected related to the
``count`` attribute of the sequence record and the ``-s`` fraction.
*Example:*
.. code-block:: bash
> obisample -s 0.5 -a seq1.fastq > seq2.fastq
Samples randomly half of the sequence records of the ``seq1.fastq`` file,
without replacement,
and saves them in the ``seq2.fastq`` file.
.. cmdoption:: -w, --without-replacement
Asks for sampling without replacement.
*Example:*
.. code-block:: bash
> obisample -s 1000 -w seq1.fasta > seq2.fasta
Samples randomly 1000 sequence records from the ``seq1.fasta`` file, without replacement
(the input file must contain at least 1000 sequences), and saves them in the ``seq2.fasta`` file.
.. include:: ../optionsSet/inputformat.txt
.. include:: ../optionsSet/defaultoptions.txt
:py:mod:`obisample` used sequence attribute
-------------------------------------------
- :doc:`count <../attributes/count>`
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