Update softwares/scripts/to-html.py

softwares/scripts/to-html.py

+import os
+import pandas
+import csv
+import json
 
+
+def get_score(jfile, entityList = ["Standard scoring"], corpus = "BB" , task = "BB-norm"):
+    dict = {"Corpus":[], "Task":[], "Pairing":[], "Score Scope":[], "Score Name": [], "Value": []}
+    data = json.load(open(jfile))
+    for d in (data['evaluation'])['global-evaluations']:
+        scorings = d['scorings']
+        for s in scorings:
+            if s['name'] in entityList:
+                for m in s['measures']:
+                    dict["Corpus"].append(corpus)
+                    dict["Task"].append(task)
+                    dict["Pairing"].append(d['name'])
+                    dict["Score Scope"].append(s['name'])
+                    dict["Score Name"].append(m['name'])
+                    dict["Value"].append(m['value'])
+    return dict
+
+
+def get_score_norm(jfile):
+    return get_score(jfile, entityList = ["Standard scoring", "Habitats", "Phenotypes", "Microorganisms"], corpus = "BB19" , task = "BB-norm")
+
+def get_score_kb(jfile):
+    return get_score(jfile, entityList = ["Standard scoring"], corpus = "BB" , task = "BB-kb")
+
+def get_score_rel(jfile):
+    return get_score(jfile, entityList = ["Standard scoring", "Lives_In and Exhibits", "Lives_In", "Exhibits"], corpus = "BB" , task = "BB-rel")
+
+# Main
+if __name__ == '__main__':
+
+    import sys
+    
+    from optparse import OptionParser, OptionGroup
+
+    optparser = OptionParser(usage="%extract data from genbank bank")
+    group = OptionGroup(optparser, "Main Options", "")
+    optparser.add_option("-t", "--file", default="None", dest="taxo_ref", help="", metavar="FILE")
+    optparser.add_option("-d", "--task", default="None", dest="db_path", help="", metavar="FILE")