ndexsignorloader 0.1.0

Python Boilerplate contains all the boilerplate you need to create a Python NDEx Content Loader package.

NDEx Signor Content Loader

Python application that loads Signor data into NDEx

This tool downloads data files from Signor and performs the following operations:

1) The text files are loaded into a network using this loadplan

2) The edge attribute direct is set to True if value is ‘t’ otherwise its set to False

3) Using values in the databasea and databaseb data files, the represents field found on each node is prefixed with uniprot: if the database value is UNIPROT and signor: if the database value is SIGNOR

4) The compartment node attribute is set to cytoplasm if its not set (which is case for all nodes in FULL-Human, Full-Rat, and Full-Mouse networks)

5) Any negative or non-numeric citations are removed from the citation edge attribute (There were multiple cases of -1 and Other). In addition, a specific PMC:## is updated to its pubmed id.

6) The layout of the network is created using the spring layout, but with additional logic that positions nodes in a vertical based on value of the compartment node attribute. The ordering is as follows:

• extracellular are placed at the top
• receptor are below extracellular
• cytoplasm are placed in the middle
• factor are below cytoplasm
• phenotypeList are placed at the bottom

7) The following network attributes are set

• name is set to data from Signor service getPathwayData.php?pathway= (except for the Full networks which have a more generic description)
• author is set to data from Signor service getPathwayData.php?pathway=
• organism is set to Human, 9606, Homo sapiens (except for Full Rat and Mouse networks)
• prov:wasGeneratedBy is set to ndexsignorloader <VERSION> (example: ndexsignorloader 1.0.0)
• prov:wasDerivedFrom set to URL to download data file
• version is set to Abbreviated day-month-year (example: 05-Jun-2019)
• description is taken from Signor service getPathwayData.php?pathway=
• rightsHolder is set to Prof. Gianni Cesareni
• rights is set to Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
• reference is set to citation for SIGNOR: a database of causal relationships between biological entities
• labels is set to data from Signor service getPathwayData.php?pathway=
• type is set to a list with pathway and if known type of pathway
• __normalizationversion is set to 0.1

Dependencies

• ndex2
• ndexutil

Compatibility

• Python 3.3+

Installation

git clone https://github.com/ndexcontent/ndexsignorloader
cd ndexsignorloader
make dist
pip install dist/ndexloadsignor*whl

Run make command with no arguments to see other build/deploy options including creation of Docker image

make

Output:

clean                remove all build, test, coverage and Python artifacts
clean-build          remove build artifacts
clean-pyc            remove Python file artifacts
clean-test           remove test and coverage artifacts
lint                 check style with flake8
test                 run tests quickly with the default Python
test-all             run tests on every Python version with tox
coverage             check code coverage quickly with the default Python
docs                 generate Sphinx HTML documentation, including API docs
servedocs            compile the docs watching for changes
testrelease          package and upload a TEST release
release              package and upload a release
dist                 builds source and wheel package
install              install the package to the active Python's site-packages
dockerbuild          build docker image and store in local repository
dockerpush           push image to dockerhub

Configuration

The ndexloadsignor.py requires a configuration file in the following format be created. The default path for this configuration is ~/.ndexutils.conf but can be overridden with --conf flag.

Format of configuration file

[<value in --profile (default ndexsignorloader)>]

user = <NDEx username>
password = <NDEx password>
server = <NDEx server(omit http) ie public.ndexbio.org>

Example configuration file

[ndexsignorloader_dev]

user = joe123
password = somepassword123
server = dev.ndexbio.org

Needed files

TODO: Add description of needed files

Usage

For information invoke ndexloadsignor.py -h

Example usage

TODO: Add information about example usage

ndexloadsignor.py # TODO Add other needed arguments here

Via Docker

Example usage

TODO: Add information about example usage

docker run -v `pwd`:`pwd` -w `pwd` coleslawndex/ndexsignorloader:0.1.0 ndexloadsignor.py --conf conf # TODO Add other needed arguments here

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.1.0 (2019-06-27)

• First release on PyPI.