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scripts/parse_harbison_data.R

@@ -130,34 +130,59 @@ combined_harbison_harmonized = combined_harbison %>%
   dplyr::rename(harbison_regulator=tf) %>%
   select(-description)
 
-combined_harbison_harmonized %>%
-  select(condition, regulator_locus_tag, target_locus_tag, effect, pvalue) %>%
-  group_by(condition, regulator_locus_tag) %>%
-  write_dataset(path = here("data/harbison/hf/data"), format = "parquet")
+harbison_db_meta <- read_csv("data/promotersetsig_db_20251127.csv",
+                             col_types = cols(composite_binding = col_character()))
 
-combined_harbison_harmonized %>%
-  select(regulator_locus_tag,regulator_symbol,
-         target_locus_tag, target_symbol,
-         condition, effect, pvalue) %>%
-  write_parquet("~/code/hf/harbison_2004/harbison_2004.parquet",
-                compression = "zstd",
-                write_statistics = TRUE,
-                chunk_size = 6226,
-                use_dictionary = c(
-                  condition = TRUE,
-                  regulator_locus_tag = TRUE,
-                  regulator_symbol = TRUE,
-                  target_locus_tag = TRUE,
-                  target_symbol = TRUE
-                )
-  )
-
-combined_harbison_harmonized %>%
-  select(harbison_locus_tag, target_locus_tag) %>%
+db_id_map = harbison_db_meta %>%
+  filter(source_name == "harbison_chip") %>%
+  select(id, regulator_locus_tag, condition) %>%
   distinct() %>%
-  write_csv("~/code/hf/harbison_2004/scripts/harbison_locus_tag_to_target_locus_tag.csv")
+  dplyr::rename(db_id = id) %>%
+  bind_rows(
+    tibble(
+      regulator_locus_tag = c("YSC0017"),
+      db_id = 0,
+      condition = c('YPD')
+      ))
+
+combined_harbison_harmonized_for_parquet = combined_harbison_harmonized %>%
+  select(regulator_locus_tag, regulator_symbol,
+         condition, target_locus_tag, target_symbol,
+         effect, pvalue) %>%
+  left_join(db_id_map) %>%
+  arrange(db_id) %>%
+  group_by(db_id) %>%
+  mutate(sample_id = cur_group_id()) %>%
+  ungroup() %>%
+  select(sample_id, db_id, regulator_locus_tag, regulator_symbol,
+         condition,
+         target_locus_tag, target_symbol,
+         effect, pvalue)
+
+
+# combined_harbison_harmonized_for_parquet %>%
+#   write_parquet("~/code/hf/harbison_2004/harbison_2004.parquet",
+#                 compression = "zstd",
+#                 write_statistics = TRUE,
+#                 chunk_size = 6226,
+#                 use_dictionary = c(
+#                   sample_id = TRUE,
+#                   condition = TRUE,
+#                   regulator_locus_tag = TRUE,
+#                   regulator_symbol = TRUE,
+#                   target_locus_tag = TRUE,
+#                   target_symbol = TRUE
+#                 )
+#   )
+#
+#
+# combined_harbison_harmonized %>%
+#   select(harbison_locus_tag, target_locus_tag) %>%
+#   distinct() %>%
+#   write_csv("~/code/hf/harbison_2004/scripts/harbison_locus_tag_to_target_locus_tag.csv")
+#
+# combined_harbison_harmonized %>%
+#   select(harbison_regulator, regulator_locus_tag) %>%
+#   distinct() %>%
+#   write_csv("~/code/hf/harbison_2004/scripts/harbison_regulator_to_regulator_locus_tag.csv")
 
-combined_harbison_harmonized %>%
-  select(harbison_regulator, regulator_locus_tag) %>%
-  distinct() %>%
-  write_csv("~/code/hf/harbison_2004/scripts/harbison_regulator_to_regulator_locus_tag.csv")