count fixes

pombase · Nov 22, 2024 · 2b274ff · 2b274ff
1 parent afc5521
commit 2b274ff
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diff --git a/change_log/count_changes.py b/change_log/count_changes.py
@@ -0,0 +1,39 @@
+import pandas
+import glob
+
+files = glob.glob("allele_*.tsv") + [
+    "description_in_db_doesnt_match_03082023.tsv",
+    "manual_cannot_fix_new_03082023.tsv",
+    "unknowns_with_correct_descriptions_10082023.tsv",
+]
+data = pandas.DataFrame()
+
+for file in files:
+    print(file)
+    df = pandas.read_csv(file, sep="\t", na_filter=False)
+    unique_columns = df[["allele_name", "allele_description"]]
+    if "change_description_to" in df.columns:
+        unique_columns.loc[:, "description_changed"] = df["change_description_to"] != ""
+    else:
+        unique_columns.loc[:, "description_changed"] = False
+    if "change_name_to" in df.columns:
+        unique_columns.loc[:, "name_changed"] = df["change_name_to"] != ""
+    data = pandas.concat([data, unique_columns])
+
+data = data.drop_duplicates()
+
+print("> alleles fixed (at most)", len(data))
+print("> alleles with description changed (at most)", data["description_changed"].sum())
+print("> alleles with name changed (at most)", data["name_changed"].sum())
+print()
+files = glob.glob("protein_*.tsv")
+data = pandas.DataFrame()
+
+for file in files:
+    df = pandas.read_csv(file, sep="\t", na_filter=False)
+    unique_columns = df[["systematic_id", "sequence_position"]]
+    data = pandas.concat([data, unique_columns])
+
+data = data.drop_duplicates()
+
+print("> modifications fixed (at most)", len(data))
diff --git a/change_log/protein_modification_residues_not_in_new_gene_structure_issue62_14072023.tsv b/change_log/protein_modification_residues_not_in_new_gene_structure_issue62_14072023.tsv
@@ -1,3 +1,4 @@
+systematic_id	primary_name	modification	evidence	sequence_position	annotation_extension	reference	taxon	date	sequence_error	change_sequence_position_to	auto_fix_comment
 SPAC3H1.05	ste24	MOD:00046	tryptic phosphopeptide mapping assay evidence used in automatic assertion	S12		PMID:30726745	4896	2019-02-05	S12	?	old_coords_fix, revision 8148: join(1938900..1939004,1939075..1940394)	
 SPAC57A7.12	ssz1	MOD:00046	experimental evidence	S12	present_during(GO:0000087)	PMID:21712547	4896	2011-06-28	S12	?	old_coords_fix, revision 8148: complement(join(1515089..1516663,1516789..1516914))	
 SPBC2F12.10	mrpl35	MOD:00047	tryptic phosphopeptide mapping assay evidence used in automatic assertion	T13		PMID:33823663	4896	2022-03-08	T13	?	old_coords_fix, revision 20110324: complement(1719551..1720663)