Add script to process COVID-19 Disease Maps

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)