Functions to use the BridgeDb webservice in Matlab. BridgeDb is a tool for identifier mapping.
Learn about BridgeDb at http://www.bridgedb.org/ and read about it in this paper:
Van Iersel, M.; Pico, A.; Kelder, T.; Gao, J.; Ho, I.; Hanspers, K.; Conklin, B.; Evelo, C. BMC Bioinformatics 2010, 11, 5, https://doi.org/10.1186/1471-2105-11-5
The DOI of this repository is 10.5281/zenodo.5550067.
License: AGPL-3
Please download Matlab first, as well as Python (instructions). For Python, check if you use a supported version (version 2.7, 3.7, and 3.8 are currently supported) On the command line (Bash/Unix users):
python -V
Check if Python is setup correctly in Matlab, from the Matlab Command Window:
pe = pyenvDownload this repository:
git clone https://github.com/bridgedb/BridgeDb-matlab.git
- Start your version of Matlab [tested with Matlab 2021A]
- Add the folder where you downloaded this code (e.g. BridgeDb-matlab) to your working directory: Right-click, 'Add to Path'/'Selected Folders and Subfolders'
- Open the folder (double click or rightclick/Open). Your Current folder in Matlab should look like this now:
- Visit the matlab online page
- Upload the folder where you donwloaded this code (e.g. BridgeDb-matlab) to your Matlab Drive.
When the upload succeeded, you should see the BridgeDb-Matlab folde rin your drive, and in you Matlab Online Instance:
- Add the folder to your working directory:
- In the Matlab command window, type the following command to check your pathway directory:
pwd- Switch to the folder containing your code (if needed):
cd('PATH/TO/FILE')- Execute the XrefsBatch mapping function on the test data, located in the 'testData' folder, as such:
xrefsBatch('BridgeDb-matlab/testData/case1-example.tsv', 'Homo sapiens', 'H')- Your results are stored in your working directory, as a file called 'mappings.csv' (located in the folder testData):
- You can view your results by double clicking the mappings.csv file in the Matlab working directory:
