IronYeasts is a project that aims to find the genes involved in iron homeostasis in pathogenic yeasts. This project is divided into 2 main parts :
We use Pipenv to develop and run Python programs in IronYeast. We invite you to ensure you have installed the following requirements before trying to use different programs:
We invite you to install pipenv to get all the necessary packages :
$ git clone https://github.com/thomasdenecker/IronYeasts.git
$ cd IronYeasts
$ pipenv install --ignore-pipfile
This project use flake8 to ensure coding style consistency (PEP8). To test python codes locally, you can use this commande line:
$ pipenv run flake8 formater.py
Have you read the "Requirements" section above?
# Clone the project
$ git clone https://github.com/thomasdenecker/IronYeasts.git
$ cd IronYeasts
$ pipenv install --ignore-pipfile
Then, we invite you to read the different READMEs proposed for each options :
--mesh
: To get link betweenn MESH Term--go
: To associate GO with its definition--gryc
: To get GRYC annotation for yeasts.To have help for formater.py
:
$ python formater.py --help
usage: formater.py [-h] [-i INPUT] [-o OUTPUT] [--mesh] [--go] [--gryc]
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
For MESH, a Mesh file (bin format find here
(dYEAR.bin, ie. d2018.bin):
ftp://nlmpubs.nlm.nih.gov/online/mesh/MESH_FILES/
asciimesh/). For GO, a GO terms file (obo format find
here : (go.obo, ie. go.obo :
http://purl.obolibrary.org/obo/go.obo). By default,
the last version.For GRYC a folder with EMBL files
-o OUTPUT, --output OUTPUT
Output file name (whithout format (.txt))
--mesh Converte raw mesh file to link table
--go Associate GO term and its definition
--gryc Generate table with all annotations of GRYC
Continuous Integration (CI) is the process of automating the build and testing of code at each commit changes.
In this project, we use Travis CI. A documentation is available here.
flake8
is tool to ensure coding style consistency (PEP8).
To run locally them with python codes
$ pipenv run flake8 formater.py
The pytest framework makes it easy to write small tests, yet scales to support complex functional testing for applications and libraries.
In coming
Coveralls is a web service to help you track your code coverage over time, and ensure that all your new code is fully covered.
A documentation is available here
In coming
We test for each change with a test file whether the output file is always the same.
diff file1.txt file2.txt
Please, see the CONTRIBUTING file.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms. See CODE_OF_CONDUCT file.
Pixel is released under the BSD-3 License. See the bundled LICENSE file for details.