comparison README.rst @ 1:0699939e6dd6 draft

"Release v0.8.4"

0:1625927fc16f

Hi, I’m GECCO!
==============

🦎 ️Overview
---------------

GECCO (Gene Cluster prediction with Conditional Random Fields) is a fast

GECCO is implemented in `Python <https://www.python.org/>`__, and
supports `all versions <https://endoflife.date/python>`__ from Python
3.6. It requires additional libraries that can be installed directly
from `PyPI <https://pypi.org>`__, the Python Package Index.

Use ```pip`` <https://pip.pypa.io/en/stable/>`__ to install GECCO on
your machine:

.. code:: console

   $ pip install gecco-tool

If you’d rather use `Conda <https://conda.io>`__, a package is available
in the ```bioconda`` <https://bioconda.github.io/>`__ channel. You can
install with:

.. code:: console

   $ conda install -c bioconda gecco

This will install GECCO, its dependencies, and the data needed to run
predictions. This requires around 100MB of data to be downloaded, so it
could take some time depending on your Internet connection. Once done,
you will have a ``gecco`` command available in your $PATH.

*Note that GECCO uses*\ `HMMER3 <http://hmmer.org/>`__\ *, which can
only run on PowerPC and recent x86-64 machines running a POSIX operating
system. Therefore, Linux and OSX are supported platforms, but GECCO will
not be able to run on Windows.*

🧬 Running GECCO
-----------------

Once ``gecco`` is installed, you can run it from the terminal by giving
it a FASTA or GenBank file with the genomic sequence you want to
analyze, as well as an output directory:

.. code:: console

   $ gecco run --genome some_genome.fna -o some_output_dir

Additional parameters of interest are:

-  ``--jobs``, which controls the number of threads that will be spawned
   by GECCO whenever a step can be parallelized. The default, *0*, will
   autodetect the number of CPUs on the machine using
   ```os.cpu_count`` <https://docs.python.org/3/library/os.html#os.cpu_count>`__.
-  ``--cds``, controlling the minimum number of consecutive genes a BGC
   region must have to be detected by GECCO (default is 3).
-  ``--threshold``, controlling the minimum probability for a gene to be
   considered part of a BGC region. Using a lower number will increase
   the number (and possibly length) of predictions, but reduce accuracy.

🏗️ Contributing
~~~~~~~~~~~~~~~~

Contributions are more than welcome! See
```CONTRIBUTING.md`` <https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md>`__
for more details.

⚖️ License
----------

1:0699939e6dd6

Hi, I’m GECCO!
==============

.. image:: https://raw.githubusercontent.com/zellerlab/GECCO/v0.6.2/static/gecco-square.png
   :target: https://github.com/zellerlab/GECCO/


🦎 ️Overview
---------------

GECCO (Gene Cluster prediction with Conditional Random Fields) is a fast

GECCO is implemented in `Python <https://www.python.org/>`__, and
supports `all versions <https://endoflife.date/python>`__ from Python
3.6. It requires additional libraries that can be installed directly
from `PyPI <https://pypi.org>`__, the Python Package Index.

Use `pip <https://pip.pypa.io/en/stable/>`__ to install GECCO on
your machine::

   $ pip install gecco-tool

If you’d rather use `Conda <https://conda.io>`__, a package is available
in the `bioconda <https://bioconda.github.io/>`__ channel. You can
install with::

   $ conda install -c bioconda gecco

This will install GECCO, its dependencies, and the data needed to run
predictions. This requires around 100MB of data to be downloaded, so it
could take some time depending on your Internet connection. Once done,
you will have a ``gecco`` command available in your $PATH.

*Note that GECCO uses* `HMMER3 <http://hmmer.org/>`__, *which can
only run on PowerPC and recent x86-64 machines running a POSIX operating
system. Therefore, Linux and OSX are supported platforms, but GECCO will
not be able to run on Windows.*

🧬 Running GECCO
-----------------

Once ``gecco`` is installed, you can run it from the terminal by giving
it a FASTA or GenBank file with the genomic sequence you want to
analyze, as well as an output directory::

   $ gecco run --genome some_genome.fna -o some_output_dir

Additional parameters of interest are:

-  ``--jobs``, which controls the number of threads that will be spawned
   by GECCO whenever a step can be parallelized. The default, *0*, will
   autodetect the number of CPUs on the machine using
   `os.cpu_count <https://docs.python.org/3/library/os.html#os.cpu_count>`__.
-  ``--cds``, controlling the minimum number of consecutive genes a BGC
   region must have to be detected by GECCO (default is 3).
-  ``--threshold``, controlling the minimum probability for a gene to be
   considered part of a BGC region. Using a lower number will increase
   the number (and possibly length) of predictions, but reduce accuracy.

🏗️ Contributing
~~~~~~~~~~~~~~~~

Contributions are more than welcome! See
`CONTRIBUTING.md <https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md>`__
for more details.

⚖️ License
----------