From c4060de768e9a71fcc8303b3f0cae78c3d99d697 Mon Sep 17 00:00:00 2001
From: dustine32 <dustine32@gmail.com>
Date: Mon, 5 Jan 2026 17:44:52 -0800
Subject: [PATCH] Swap unnamed_gene field for has_gene_symbol for #89

---
 data_conversion/Makefile               |  2 +-
 data_conversion/gene_info_from_gafs.py | 21 ++++++++-------------
 2 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/data_conversion/Makefile b/data_conversion/Makefile
index 4f0a8de..1eb8bf0 100644
--- a/data_conversion/Makefile
+++ b/data_conversion/Makefile
@@ -126,7 +126,7 @@ export DEBUG_INDENT ?= 0
 	touch $@
 
 .PRECIOUS: %/annotations.csv
-%/annotations.csv: %/export_annotations.tsv
+%/annotations.csv: %/export_annotations.touch
 	sed -E 's/UNKNOWN:[0-9]+//g' $*/export_annotations.tsv > $@
 
 .PRECIOUS: %/functionome_release.gaf
diff --git a/data_conversion/gene_info_from_gafs.py b/data_conversion/gene_info_from_gafs.py
index 4a07821..f904204 100644
--- a/data_conversion/gene_info_from_gafs.py
+++ b/data_conversion/gene_info_from_gafs.py
@@ -45,35 +45,29 @@ def extract_from_annotation_gaf(self, annotation_gafs):
                         continue
                     self.add_genes_from_row(r)
 
-    @staticmethod
-    def handle_gene_name(incoming_gene_name: str) -> str:
-        if incoming_gene_name == "Uncharacterized protein":
-            return "Unnamed gene"
-        return incoming_gene_name
-
     def add_genes_from_row(self, csv_row: List):
         gene_id = "{}:{}".format(csv_row[0], csv_row[1])
         gene_symbol = csv_row[2]
-        gene_name = self.handle_gene_name(csv_row[9])
+        gene_name = csv_row[9]
         gene_taxon = csv_row[12].replace("taxon:", "")
         self.gene_info_dict[gene_id] = {
             "gene": gene_id,
             "gene_symbol": gene_symbol,
             "gene_name": gene_name,
-            "unnamed_gene": gene_name == "Unnamed gene",
+            "has_gene_symbol": gene_symbol != gene_id.split(":", maxsplit=1)[1],
             "taxon_id": gene_taxon,
         }
         with_from_raw = csv_row[7]
         if "|" in with_from_raw:
             with_gene_id = with_from_raw.split("|", maxsplit=1)[1]
             with_gene_symbol = csv_row[18]
-            with_gene_name = self.handle_gene_name(csv_row[19])
+            with_gene_name = csv_row[19]
             with_gene_taxon_id = csv_row[20].replace("taxon:", "")
             self.gene_info_dict[with_gene_id] = {
                 "gene": with_gene_id,
                 "gene_symbol": with_gene_symbol,
                 "gene_name": with_gene_name,
-                "unnamed_gene": with_gene_name == "Unnamed gene",
+                "has_gene_symbol": with_gene_symbol != with_gene_id.split(":", maxsplit=1)[1],
                 "taxon_id": with_gene_taxon_id,
             }
 
@@ -99,14 +93,15 @@ def fill_in_gene_symbol_name(self, gene_dat_file: str):
                             "taxon_id": "9606",
                         }
                     gene_symbol = r[2]
-                    gene_name = self.handle_gene_name(r[1])
+                    gene_name = r[1]
                     if self.gene_info_dict[gene_id]["gene_symbol"] == "":
                         self.gene_info_dict[gene_id]["gene_symbol"] = gene_symbol
+                        self.gene_info_dict[gene_id]["has_gene_symbol"] = True
                     if self.gene_info_dict[gene_id]["gene_symbol"] == "":
                         # Duplicating symbol filling logic from createGAF.pl
                         self.gene_info_dict[gene_id]["gene_symbol"] = gene_id.split(":", maxsplit=1)[1]
+                        self.gene_info_dict[gene_id]["has_gene_symbol"] = False
                     self.gene_info_dict[gene_id]["gene_name"] = gene_name
-                    self.gene_info_dict[gene_id]["unnamed_gene"] = gene_name == "Unnamed gene"
                     self.gene_info_dict[gene_id]["long_id"] = long_id
                     # self.gene_info_dict[gene_id]["taxon_id"] = species_oscode_to_taxon_id[oscode]
 
@@ -146,7 +141,7 @@ def gene_info_list(self):
                 "gene": gene,
                 "gene_symbol": gene_info["gene_symbol"],
                 "gene_name": gene_info["gene_name"],
-                "unnamed_gene": gene_info["unnamed_gene"],
+                "has_gene_symbol": gene_info["has_gene_symbol"],
                 "taxon_id": gene_info["taxon_id"],
                 "panther_family": gene_info.get("panther_family"),  # can be None
                 "long_id": gene_info.get("long_id"),  # can be None