paper cleanup

paper/combine_csv.py

@@ -6,6 +6,6 @@
     df = pd.read_csv(filename)
     df = df[columns]
     df_list.append(df)
-df_combined.sort_values("date").to_csv("combo.csv", index=False)
+df_combined.sort_values("date").to_csv("hgvs_searches_combined.csv", index=False)
 
 

paper/investigate_fails.py

@@ -0,0 +1,29 @@
+#!/bin/env python3
+
+import math
+import re
+import sys
+import pandas as pd
+from pysam.libcfaidx import FastaFile
+import pyhgvs
+from cdot.pyhgvs.pyhgvs_transcript import JSONPyHGVSTranscriptFactory
+
+
+def main():
+    if len(sys.argv) != 1:
+        sys.stderr.write(f"Usage {sys.argv[0]} hgvs_searches_combined.csv\n")
+        sys.exit(1)
+
+    filename = sys.argv[1]
+    df = pd.read_csv(filename)
+
+    non_resolve_mask = df["can_resolve"] is False
+    hgvs_errors_df = df[non_resolve_mask]
+
+    genome = FastaFile("/data/annotation/fasta/GCF_000001405.25_GRCh37.p13_genomic.fna.gz")
+    factory = JSONPyHGVSTranscriptFactory(["/home/dlawrence/Downloads/cdot-0.2.12.refseq.grch37_grch38.json.gz",
+                                           "/home/dlawrence/Downloads/cdot-0.2.12.ensembl.grch37_grch38.json.gz"])
+
+
+if __name__ == "__main__":
+    main()