ndexstringloader 0.1.0

Tools

• ndexloadstring.py – Loads STRING into NDEx

Dependencies

• ndex2 3.1.0a1

• ndexutil 0.2.0a1

Compatibility

• Python 3.3+

Installation

git clone https://github.com/vrynkov/ndexstringloader
cd ndexstringloader
make dist
pip install dist/ndexloadstring*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 ndexloadstring.py requires a configuration file to be created. The default path for this configuration is ~/.ndexutils.conf but can be overridden with --conf flag.

Configuration file

Networks listed in [network_ids] section need to be visible to the user

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

[prod]
user = joe123 _prod
password = somepassword123_prod
server = prod.ndexbio.org

[network_ids]
style = 9c23e193-5d73-11e9-8c69-525400c25d22
hi_confidence_style = 9c100b71-5d73-11e9-8c69-525400c25d22
full = a57b23c5-65fe-11e9-8c69-525400c25d22
hi_confidence = 311b0e5f-6570-11e9-8c69-525400c25d22

[source]
ProteinLinksFile = https://stringdb-static.org/download/protein.links.full.v11.0/9606.protein.links.full.v11.0.txt.gz
NamesFile = https://string-db.org/mapping_files/STRING_display_names/human.name_2_string.tsv.gz
EntrezIdsFile = https://stringdb-static.org/mapping_files/entrez/human.entrez_2_string.2018.tsv.gz
UniprotIdsFile = https://string-db.org/mapping_files/uniprot/human.uniprot_2_string.2018.tsv.gz

[input]
full_file_name = 9606.protein.links.full.v11.0.txt
entrez_file = human.entrez_2_string.2018.tsv
names_file = human.name_2_string.tsv
uniprot_file = human.uniprot_2_string.2018.tsv

[output]
output_tsv_file_name = 9606.protein.links.full.v11.0.tsv.txt
output_hi_conf_tsv_file_name = 9606.protein.links.full.v11.0.hi_conf.tsv.txt

Needed files

Load plan is required for running this script. string_plan.json found at ndexstringloader/ndexstringloader can be used for this purpose.

Usage

For information invoke ndexloadstring.py -h

Example usage

Here is how this command can be run for dev and prod targets:

ndexloadstring.py --loadplan loadplan.json  --profile dev

ndexloadstring.py --loadplan loadplan.json  --profile prod

docker run -v `pwd`:`pwd` -w `pwd` vrynkov/ndexstringloader:0.1.0 ndexloadstring.py --conf conf # TODO Add other needed arguments here

Credits

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