diff --git a/scripts/covid19_diseasemaps/process_covid19_diseasemaps.py b/scripts/covid19_diseasemaps/process_covid19_diseasemaps.py new file mode 100644 index 000000000..e447dd1a8 --- /dev/null +++ b/scripts/covid19_diseasemaps/process_covid19_diseasemaps.py @@ -0,0 +1,25 @@ +import json +import tqdm +from mira.modeling.amr.regnet import template_model_to_regnet_json +from mira.sources.sif import template_model_from_sif_url + + +models = ['Apoptosis', 'Coagulation-pathway', 'ER_Stress', 'ETC', 'E_protein', + 'HMOX1_Pathway', 'IFN-lambda', 'Interferon1', 'JNK_pathway', + 'Kynurenine_pathway', 'NLRP3_Activation', 'Nsp14', 'Nsp4_Nsp6', + 'Nsp9_protein', 'Orf10_Cul2_pathway', 'Orf3a', 'PAMP_signaling', + 'Pyrimidine_deprivation', 'RTC-and-transcription', + 'Renin_angiotensin', 'TGFB_pathway', 'Virus_replication_cycle'] + + +SIF_URL_BASE = ('https://git-r3lab.uni.lu/covid/models/-/raw/master/' + 'Executable%20Modules/SBML_qual_build/sif') + + +if __name__ == "__main__": + for model in tqdm.tqdm(models): + url = f'{SIF_URL_BASE}/{model}_stable.sif' + tm = template_model_from_sif_url(url) + regnet = template_model_to_regnet_json(tm) + with open(f'{model}.json', 'w') as fh: + json.dump(regnet, fh, indent=1) diff --git a/scripts/process_covid19_diseasemaps.py b/scripts/process_covid19_diseasemaps.py deleted file mode 100644 index e69de29bb..000000000