The central software of gDADs (Gene-Disease Association Database Search-tool) is written in Python script. It seeks to streamline the process of enrichment analysis of a set of genes awarded from a differential expression study.
To reference gDADs see the following faux article.
These instructions will get you a copy of the software, and associated files, on your local machine for testing purposes (see section Running tests).
Disclaimer: gDADs was developed on a Linux system (Ubuntu 18.04.4 LTS) and should preferably be run on a Linux distribution of similar architecture. It might work on macOS, but is not compatible with Windows (as of version 1.0.1).
Regrettably, no Anaconda environment file can be supplied at the moment, due to local update issues.
The command-line executable was written in Python version 3.6.9, and only uses standard modules in the current iteration (version 1.0.1).
It was intended for GOATOOLS to be implemented in the software, but this fell outside the scope of the project. Instead, a rudimentary function was added to gDADs version 1.0.1, tested in subsection Running tests.
Start by either cloning the repository using git (code below), or downloading it directly from this page.
git clone https://github.com/yogogoba/gdads.git
This should be enough to run gDADs by calling the script located in the sub-directory /scr/. If it needs to be turned into an executable, use:
chmod /path/to/scr/gDADs +x
To link to your user bin folder, and run it as a command-line command:
ln -s ~/path/to/scr/gDADs ~/bin
To make sure that it is working, run it as follows to get some further information (where the first example requires linking it to your ~/bin):
gDADs -h
or,
~/path/to/scr/gDADs -h
or,
python3 ~/path/to/scr/gDADs -h
Testing can be done by utilizing the files contained within /data/test_in/. These hold example IDs, and should be specified with [-i <input file>], potentially using [-I]. The latter is needed to specify ID format, unless it is of default type ("gene_symbol"). The attained output files can then be compared to the files found in /data/test_out/.
Test basic functionality.
~/path/to/scr/gDADs -i ~/path/to/data/test_in/deg_entrez.txt -I entrez_id
Test GO term function, where domain type is specified with [-g <ontology_domain>]. See [-h] for alternatives. By default this generates the regular gene-disease association output as well, but this can be silenced using [-silence_associations].
~/path/to/scr/gDADs -i ~/path/to/data/test_in/deg_symbol.txt -g "go_process"
Test search function.
~/path/to/scr/gDADs -s "hear"
- The command-line interface SQLite software (sqlite3 3.22.0) was used to create the SQLite database.
- Tables were created from edited versions of the below files.
The database source files were trimmed to limit the scope and size, and enable upload to GitHub. They were reduced by first limiting the curated_gene_disease_associations.tsv by only including genes which were associated with inflammation. This was then further trimmed by matching the leftover IDs with those of the other source files. These files can be found within /data/db_table_data/.
- Joel Ströbaek
See LICENCE file for information.