add parse.py

downloads-generation/data_published/parse.py

+"""
+Parse various publications' supplementary tables
+"""
+import sys
+import argparse
+
+import pandas
+
+import mhcnames
+
+
+def normalize_allele_name(s):
+    try:
+        return mhcnames.normalize_allele_name(s)
+    except Exception:
+        return "UNKNOWN"
+
+
+parser = argparse.ArgumentParser(usage=__doc__)
+
+parser.add_argument(
+    "--format",
+    metavar="PMID",
+    required=True,
+    help="pubmed ID of paper to parse")
+parser.add_argument(
+    "--input",
+    required=True,
+    help="Input data")
+parser.add_argument(
+    "--out-csv",
+    required=True,
+    help="Output file to write")
+
+parser.add_argument(
+    "--out-csv",
+    required=True,
+    help="Result file")
+
+
+PARSERS = {}
+
+# Di Marco et al 2017
+def parse_28904123(input):
+    import ipdb ; ipdb.set_trace()
+
+PARSERS["28904123"] = parse_28904123
+
+# Illing et al 2018
+def parse_30410026(input):
+    import ipdb ; ipdb.set_trace()
+
+PARSERS["30410026"] = parse_30410026
+
+# Mobbs et al 2017
+def parse_28855257(input):
+    import ipdb ; ipdb.set_trace()
+
+PARSERS["28855257"] = parse_28855257
+
+# Ramarathinam et al 2018
+def parse_29437277(input):
+    import ipdb ; ipdb.set_trace()
+
+PARSERS["29437277"] = parse_29437277
+
+# Pymm et al 2017
+def parse_28218747(input):
+    import ipdb ; ipdb.set_trace()
+
+PARSERS["28218747"] = parse_28218747
+
+
+def run():
+    args = parser.parse_args(sys.argv[1:])
+
+    if args.input.endswith(".xlsx"):
+        handle = pandas.read_excel(args.input, sheet_name=None)
+    else:
+        raise ValueError("Unsupported input: %s" % args.input)
+
+    parse_function = PARSERS.get(args.format)
+    if not parse_function:
+        raise ValueError("Unsupported format: %s" % args.format)
+
+    result = parse_function(handle)
+
+    result.to_csv(args.out_csv, index=False)
+    print("Wrote dataframe of shape %s: %s" % (result.shape, args.out_csv))
+
+if __name__ == '__main__':
+    run()