Mercurial > repos > althonos > gecco

comparison README.rst @ 1:0699939e6dd6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"Release v0.8.4"
author althonos
date Sun, 21 Nov 2021 17:00:40 +0000
parents 1625927fc16f
children e618ab1c78d9
comparison
equal deleted inserted replaced
0:1625927fc16f 1:0699939e6dd6
1 Hi, I’m GECCO! 1 Hi, I’m GECCO!
2 ============== 2 ==============
3
4 .. image:: https://raw.githubusercontent.com/zellerlab/GECCO/v0.6.2/static/gecco-square.png
5 :target: https://github.com/zellerlab/GECCO/
6
3 7
4 🦎 ️Overview 8 🦎 ️Overview
5 --------------- 9 ---------------
6 10
7 GECCO (Gene Cluster prediction with Conditional Random Fields) is a fast 11 GECCO (Gene Cluster prediction with Conditional Random Fields) is a fast
18 GECCO is implemented in `Python <https://www.python.org/>`__, and 22 GECCO is implemented in `Python <https://www.python.org/>`__, and
19 supports `all versions <https://endoflife.date/python>`__ from Python 23 supports `all versions <https://endoflife.date/python>`__ from Python
20 3.6. It requires additional libraries that can be installed directly 24 3.6. It requires additional libraries that can be installed directly
21 from `PyPI <https://pypi.org>`__, the Python Package Index. 25 from `PyPI <https://pypi.org>`__, the Python Package Index.
22 26
23 Use ```pip`` <https://pip.pypa.io/en/stable/>`__ to install GECCO on 27 Use `pip <https://pip.pypa.io/en/stable/>`__ to install GECCO on
24 your machine: 28 your machine::
25
26 .. code:: console
27 29
28 $ pip install gecco-tool 30 $ pip install gecco-tool
29 31
30 If you’d rather use `Conda <https://conda.io>`__, a package is available 32 If you’d rather use `Conda <https://conda.io>`__, a package is available
31 in the ```bioconda`` <https://bioconda.github.io/>`__ channel. You can 33 in the `bioconda <https://bioconda.github.io/>`__ channel. You can
32 install with: 34 install with::
33
34 .. code:: console
35 35
36 $ conda install -c bioconda gecco 36 $ conda install -c bioconda gecco
37 37
38 This will install GECCO, its dependencies, and the data needed to run 38 This will install GECCO, its dependencies, and the data needed to run
39 predictions. This requires around 100MB of data to be downloaded, so it 39 predictions. This requires around 100MB of data to be downloaded, so it
40 could take some time depending on your Internet connection. Once done, 40 could take some time depending on your Internet connection. Once done,
41 you will have a ``gecco`` command available in your $PATH. 41 you will have a ``gecco`` command available in your $PATH.
42 42
43 *Note that GECCO uses*\ `HMMER3 <http://hmmer.org/>`__\ *, which can 43 *Note that GECCO uses* `HMMER3 <http://hmmer.org/>`__, *which can
44 only run on PowerPC and recent x86-64 machines running a POSIX operating 44 only run on PowerPC and recent x86-64 machines running a POSIX operating
45 system. Therefore, Linux and OSX are supported platforms, but GECCO will 45 system. Therefore, Linux and OSX are supported platforms, but GECCO will
46 not be able to run on Windows.* 46 not be able to run on Windows.*
47 47
48 🧬 Running GECCO 48 🧬 Running GECCO
49 ----------------- 49 -----------------
50 50
51 Once ``gecco`` is installed, you can run it from the terminal by giving 51 Once ``gecco`` is installed, you can run it from the terminal by giving
52 it a FASTA or GenBank file with the genomic sequence you want to 52 it a FASTA or GenBank file with the genomic sequence you want to
53 analyze, as well as an output directory: 53 analyze, as well as an output directory::
54
55 .. code:: console
56 54
57 $ gecco run --genome some_genome.fna -o some_output_dir 55 $ gecco run --genome some_genome.fna -o some_output_dir
58 56
59 Additional parameters of interest are: 57 Additional parameters of interest are:
60 58
61 - ``--jobs``, which controls the number of threads that will be spawned 59 - ``--jobs``, which controls the number of threads that will be spawned
62 by GECCO whenever a step can be parallelized. The default, *0*, will 60 by GECCO whenever a step can be parallelized. The default, *0*, will
63 autodetect the number of CPUs on the machine using 61 autodetect the number of CPUs on the machine using
64 ```os.cpu_count`` <https://docs.python.org/3/library/os.html#os.cpu_count>`__. 62 `os.cpu_count <https://docs.python.org/3/library/os.html#os.cpu_count>`__.
65 - ``--cds``, controlling the minimum number of consecutive genes a BGC 63 - ``--cds``, controlling the minimum number of consecutive genes a BGC
66 region must have to be detected by GECCO (default is 3). 64 region must have to be detected by GECCO (default is 3).
67 - ``--threshold``, controlling the minimum probability for a gene to be 65 - ``--threshold``, controlling the minimum probability for a gene to be
68 considered part of a BGC region. Using a lower number will increase 66 considered part of a BGC region. Using a lower number will increase
69 the number (and possibly length) of predictions, but reduce accuracy. 67 the number (and possibly length) of predictions, but reduce accuracy.
93 91
94 🏗️ Contributing 92 🏗️ Contributing
95 ~~~~~~~~~~~~~~~~ 93 ~~~~~~~~~~~~~~~~
96 94
97 Contributions are more than welcome! See 95 Contributions are more than welcome! See
98 ```CONTRIBUTING.md`` <https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md>`__ 96 `CONTRIBUTING.md <https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md>`__
99 for more details. 97 for more details.
100 98
101 ⚖️ License 99 ⚖️ License
102 ---------- 100 ----------
103 101