Python application for loading STRING data into NDEx.
This tool downloads and unpacks the STRING files below
9606.protein.links.full.v11.0.txt.gz
generates a new tsv file, transforms it to CX, and uploads it to NDEx server.
1) Below is an example of a record from 9606.protein.links.full.v11.0.txt.gz
9606.ENSP00000261819 9606.ENSP00000353549 0 0 0 0 0 102 90 987 260 900 0 754 622 999
To generate a STRING network, the loader reads rows from that file one by one and compares the value of the last
column combined_score with the value cutoffscore argument. The row is not added to the network generated in case
combined_score is less than cutoffscore.
2) If combined_score is no than less cutoffscore, the loader process two first columns
column 1 - protein1 (9606.ENSP00000261819) column 2 - protein2 (9606.ENSP00000353549)
When processing first column protein1, the script
replaces Ensembl Id with a display name, for example 9606.ENSP00000261819 becomes ANAPC5. Mapping of
display names to Enseml Ids is found in
human.name_2_string.tsv.gz
uses human.uniprot_2_string.2018.tsv.gz
to create represents value. For example, represents for 9606.ENSP00000261819 is uniprot:Q9UJX4
uses human.entrez_2_string.2018.tsv.gz
to create list of aliases for the current protein. Thus, list of aliases for 9606.ENSP00000261819 is
ncbigene:51433|ensembl:ENSP00000261819
3) The second column protein2 is processed the same way as column 1.
4) In the generated tsv file, protein1 and protein2 values from the original file are replaced with
protein_display_name_1 represents_1 alias_1 protein_display_name_2 represents_2 alias_2
- ndex2
- ndexutil
- Python 3.3+
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
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 hi_confidence = 311b0e5f-6570-11e9-8c69-525400c25d22 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 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_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 [prod] user = joe123 _prod password = somepassword123_prod server = prod.ndexbio.org hi_confidence = 311b0e5f-6570-11e9-8c69-525400c25d22 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 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_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
Load plan is required for running this script. string_plan.json found at ndexstringloader/ndexstringloader can be used for this purpose.
For information invoke ndexloadstring.py -h
Example usage
Here is how this command can be run for dev and prod targets:
ndexloadstring.py --profile dev ndexloadstring.py --profile prod
Example usage
TODO: Add information about example usage
docker run -v `pwd`:`pwd` -w `pwd` vrynkov/ndexstringloader:0.1.0 ndexloadstring.py --conf conf # TODO Add other needed arguments here
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.