fixing chromosome names in id 762 to ucsc

genome_map/batch=run_7269/part-0.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:8b00e75f122d84ee025ac416bedd1dc3f5ea75cb742ab07fdd326a29bb750ecf
-size 983822
+oid sha256:b14d11fb9f1677067fd60868851b2bea8562f6c8e47ec839c4fd89af8888436a
+size 974357

scripts/quantify_regions.R

@@ -433,12 +433,66 @@ enrichment_analysis <- function(experiment_gr,
 
 # Example Usage -----------------------------------------------------------
 
-# This is a template for how to use these functions
-# Uncomment and modify for your actual data
+# add another batch to the genome map
+
+genomic_features = arrow::read_parquet("~/code/hf/yeast_genome_resources/brentlab_features.parquet")
 
 genome_map_replicate_ds = arrow::open_dataset("~/code/hf/callingcards/genome_map")
 genome_map_replicate_meta = arrow::read_parquet("~/code/hf/callingcards/genome_map_meta.parquet")
 
+max_gm_id = max(genome_map_replicate_meta$id)
+
+rs_rl_map = dplyr::select(genomic_features,
+                          regulator_locus_tag = locus_tag,
+                          regulator_symbol = symbol) %>%
+    filter(regulator_symbol %in% c("MED2", "XBP1", "UME1", "RPH1"))
+
+
+run_7488_qbed = list.files("~/htcf_local/cc/yeast/results/run_7488/hops",
+                           "*qbed",
+                           full.names=TRUE)
+run_7489_qbed = list.files("~/htcf_local/cc/yeast/results/run_7489/hops",
+                           "*qbed",
+                           full.names=TRUE)
+
+new_metadata = read_tsv("~/htcf_local/cc/yeast/data/run_7488/JP094_barcodes.txt",
+                    col_names = c("regulator", "bc1", "bc2")) %>%
+    mutate(condition = ifelse(str_detect(regulator, "∆"), "del_MSN2", "standard")) %>%
+    mutate(regulator_symbol = str_remove(regulator, "∆.*")) %>%
+    mutate(batch = "run_7488") %>%
+    bind_rows(
+        read_tsv("~/htcf_local/cc/yeast/data/run_7489/JP095_barcodes.txt",
+                 col_names = c("regulator", "bc1", "bc2")) %>%
+            mutate(condition = ifelse(str_detect(regulator, "∆"), "del_MSN2", "standard")) %>%
+            mutate(regulator_symbol = str_remove(regulator, "∆.*")) %>%
+            mutate(batch = "run_7489")) %>%
+    mutate(binding_id = "NA") %>%
+    left_join(rs_rl_map) %>%
+    mutate(replicate = 1,
+           notes = "none") %>%
+    mutate(id = max_gm_id + row_number()) %>%
+    dplyr::select(id, binding_id, regulator_locus_tag, regulator_symbol,
+                    batch, replicate, notes, condition) %>%
+    left_join(
+        tibble(qbed = c(run_7488_qbed, run_7489_qbed)) %>%
+            mutate(batch = str_extract(basename(qbed), "run_\\d+")) %>%
+            mutate(condition = ifelse(str_detect(basename(qbed), "del"), "del_MSN2", "standard")) %>%
+            mutate(regulator_symbol = str_remove_all(basename(qbed), "run_\\d+_|del.*|.qbed")) %>%
+            filter(regulator_symbol != "undetermined")
+    )
+
+new_data = map(c(run_7488_qbed, run_7489_qbed), ~{
+    in_path = file.path("~/htcf_local/cc/yeast/results/")
+    read_tsv(.)
+})
+
+
+
+
+# This is a template for how to use these functions
+# Uncomment and modify for your actual data
+
+
 background_gr <- read_tsv("~/code/hf/callingcards/adh1_background_ucsc.qbed") %>%
   mutate(id = "adh1_bg",
          score = scales::rescale(depth, to = c(1,1000))) %>%
@@ -449,7 +503,6 @@ regions_gr <- read_tsv("~/code/hf/yeast_genome_resources/yiming_promoters.bed",
                         col_names = c('chr', 'start', 'end', 'locus_tag', 'score', 'strand'))  %>%
   bed_to_granges()
 
-genomic_features = arrow::read_parquet("~/code/hf/yeast_genome_resources/brentlab_features.parquet")
 
 # # Run analysis with deduplication (default for calling cards)
 results_replicates = map(genome_map_meta$id, ~{