Example source code to automatically process data from the FDC.
Usage:
Step 1: please login to FDC website with Google Chrome with your credential.
If you are using other browsers, please change the line 7 at download_treatment.py
Step 2: run this command. Input your keychain password if prompted
./download_treatment.py test/result.example.txt
If you want to process all CytoSig data, we also included all result catalog files in the same folder (result.Cytokine.txt, result.Chemokine.txt, result.Growth_factor.txt, result.Inhibitory.txt)
As the result, in the test folder, you will see two new folders:
1, raw: raw data download from FDC server, including meta data annotation and processed expression matrices (FDC can automatically generate it from public repositories).
2, diff: differential expression profiles. Each file will also include a count map file, for the number of replicates per condition. If a dataset has Sub Condition annotated, a *.sep.gz will also be generated through merging replicates at Sub Condition levels.
This example code only works for treatment experiment with annotation fields, Treatment, Condition, Sub Condition, Dose, and Duration. For other curation scheme, you need to design your own program.
For unknown reason, the python requests library will get stuck without timeout parameter. If any users know the reason, please contact me at pengj@alumni.princeton.edu