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.. automodule:: oligotag
:py:mod:`oligotag` specific options
-----------------------------------
.. cmdoption:: -L <filename>, --oligo-list=<filename>
Filename containing a list of oligonucleotides. `oligotag` selects within this list
the oligonucleotides that match the specified options.
.. CAUTION:: Cannot be used with the ``-s`` option.
.. cmdoption:: -s ###, --oligo-size=###
Size of oligonucleotides to be generated.
.. CAUTION:: Cannot be used with the ``-L`` option.
.. WARNING:: A size equal or greater than eight often leads to a very long
computing time and requires a large amount of memory.
.. cmdoption:: -f ###, --family-size=###
Minimal size of the oligonucleotide family to be generated.
.. cmdoption:: -d ###, --distance=###
Minimal Hamming distance (number of differences)
between two oligonucleotides.
.. cmdoption:: -g ###, --gc-max=###
Maximum number of G or C in the oligonucleotides.
.. cmdoption:: -a <IUPAC_PATTERN>, --accepted=<IUPAC_PATTERN>
Selected oligonucleotides are constrained by the given pattern
(only :doc:`IUPAC <../iupac>` symbols are allowed).
.. CAUTION:: pattern length must have the same length as oligonucleotides.
.. cmdoption:: -r <IUPAC_PATTERN>, --rejected=<IUPAC_PATTERN>
Selected oligonucleotides do not match the given pattern
(only :doc:`IUPAC <../iupac>` symbols are allowed).
.. CAUTION:: pattern length must have the same length as oligonucleotides.
.. cmdoption:: -p ###, --homopolymer=###
Selected oligonucleotides do not contain any homopolymer
longer than the specified length.
.. cmdoption:: -P ###, --homopolymer-min=###
Selected oligonucleotides contain at least one homopolymer longer
or equal to the specified length.
.. cmdoption:: -T <seconde>, --timeout=<seconde>
Timeout to identify a set of oligonucleotides of required size,
as defined by the ``-f`` option.
.. include:: ../optionsSet/defaultoptions.txt
Examples
--------
*Example 1:*
.. code-block:: bash
> oligotag -s 5 -f 24 -d 3 -g 3 -p 2 > mytags.txt
Searches for a family of at least 24 oligonucleotides of a length of 5 nucleotides,
with at least 3 differences among them, with a maximum of 3 C/G, and without
homopolymers longer than 2. The resulting list of oligonucleotides is saved in
the ``mytags.txt`` file.
*Example 2:*
.. code-block:: bash
> oligotag -d 5 -L my_oligos.txt -f 10 -p 1
Searches for a subset of at least 10 oligonucleotides listed in the ``my_oligos.txt`` file, with
at least 5 differences among them, and without homopolymers. The ``my_oligos.txt`` file must
contain a set of oligonucleotides of the same length, with only one oligonucleotide per line.
The resulting list of oligonucleotides is printed on the terminal window.
*Example 3:*
.. code-block:: bash
> oligotag -s 7 -f 96 -d 3 -p 1 -r cnnnnnn > mytags.txt
Searches for a family of at least 96 oligonucleotides of a length of 7 nucleotides,
with at least 3 differences among them, without homopolymers, and without a ``C`` in
the first position. The resulting list is saved in the ``mytags.txt`` file.
*Example 4:*
.. code-block:: bash
> oligotag -s 9 -f 24 -d 3 -a yryryryry > mytags.txt
Searches for a family of at least 24 oligonucleotides of a length of 9 nucleotides,
with at least 3 differences among them, and an alternation of pyrimidines and purines.
The resulting list is saved in the ``mytags.txt`` file. Because of the
constraints imposed by the ``-a`` option, it is possible to compute longer oligonucleotides
in a reasonable time.
Reference
---------
E. Coissac. Oligotag: a program for designing sets of tags for next-generation sequencing of multiplexed samples. Methods Mol Biol, 888:13-31, 2012.
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