Update scripts/parse_mcisaac_data.R

scripts/parse_mcisaac_data.R

@@ -86,20 +86,55 @@ mcisaac_GeneName_to_target_locus_tag = mcisaac_for_parquet %>%
   select(GeneName, target_locus_tag) %>%
   distinct()
 
-mcisaac_for_parquet %>%
-    select(regulator_locus_tag, regulator_symbol, target_locus_tag, target_symbol,
-           time, mechanism, restriction, date, strain,
-           ends_with("median"), starts_with("log2")) %>%
-write_parquet("~/code/hf/hackett_2020/hackett_2020.parquet",
-              compression = "zstd",
-              write_statistics = TRUE,
-              use_dictionary = c(
-                regulator_locus_tag = TRUE,
-                regulator_symbol = TRUE,
-                target_locus_tag = TRUE,
-                target_symbol = TRUE,
-                time = TRUE,
-                mechanism = TRUE,
-                restriction = TRUE,
-                date = TRUE,
-                strain = TRUE))
+# mcisaac_for_parquet %>%
+#   select(regulator_locus_tag, time, mechanism, restriction, date, strain,
+#          target_locus_tag, ends_with("median"), starts_with("log2")) %>%
+#   group_by(regulator_locus_tag, time, mechanism, restriction, date, strain) %>%
+#   write_dataset(path = here("data/mcisaac/hf/data"), format = "parquet")
+
+db_mcisaac_data = read_csv("data/mcisaac/database_mcisaac_20251126.csv") %>%
+  select(id, regulator_locus_tag, mechanism, restriction, time, notes) %>%
+  mutate(
+    strain = trimws(str_extract(notes, "(?<=strain_id:)[^;]+")),
+    date = trimws(str_extract(notes, "(?<=date:)[^;]+")),
+    mechanism = toupper(mechanism)) %>%
+  select(-notes) %>%
+  dplyr::rename(db_id = id) %>%
+  bind_rows(
+    mcisaac_for_parquet %>%
+      filter(regulator_locus_tag %in% c("GEV", "Z3EV")) %>%
+      select(regulator_locus_tag, time, mechanism,
+             restriction, date, strain) %>%
+      distinct() %>%
+      mutate(db_id = 0)) %>%
+  arrange(db_id) %>%
+  mutate(sample_id = row_number())
+
+final_mcisaac = mcisaac_for_parquet %>%
+  left_join(db_mcisaac_data) %>%
+  select(sample_id, db_id,
+         regulator_locus_tag, regulator_symbol,
+         target_locus_tag, target_symbol,
+         time, mechanism, restriction, date, strain,
+         ends_with("median"), starts_with("log2"))
+
+# note! verify before overwriting that the sample_id for the unique sample
+# tuple is the same as it is in the current hackett_2020, or that any changes
+# are intentional
+
+# final_mcisaac %>%
+#   write_parquet("~/code/hf/hackett_2020/hackett_2020.parquet",
+#               compression = "zstd",
+#               chunk_size = 6175,
+#               write_statistics = TRUE,
+#               use_dictionary = c(
+#                 sample_id = TRUE,
+#                 regulator_locus_tag = TRUE,
+#                 regulator_symbol = TRUE,
+#                 target_locus_tag = TRUE,
+#                 target_symbol = TRUE,
+#                 time = TRUE,
+#                 mechanism = TRUE,
+#                 restriction = TRUE,
+#                 date = TRUE,
+#                 strain = TRUE))