delete main globi scripts and references to globi in other scripts

viralemergence · Oct 11, 2024 · fb645be · fb645be
1 parent 5892a1c
commit fb645be
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Showing 6 changed files with 4 additions and 196 deletions.
diff --git a/Code/02_1b_Digest GenBank.R b/Code/02_1b_Digest GenBank.R
@@ -45,8 +45,8 @@ gb %<>% dplyr::rename(HostOriginal = "Host") %>%
                                  "Myxini",
                                  "Reptilia") | HostOrder %in% 
            c("Testudines", "Crocodylia"))
-            # Reptilia is defunct but left in case GLOBI has something on it 
-            # or it"s reinstituted or something weird
+            # Reptilia is defunct but left in case
+            # it's reinstituted or something weird
 
 # get vector of the species names 
 virus_vec <- gb %>% 

diff --git a/Code/02_3a_Download GLOBI.R b/Code/02_3a_Download GLOBI.R
diff --git a/Code/02_3b_Digest GLOBI.R b/Code/02_3b_Digest GLOBI.R
diff --git a/Code/02_3c_Format GLOBI.R b/Code/02_3c_Format GLOBI.R
diff --git a/Code/03_Merge clean files.R b/Code/03_Merge clean files.R
@@ -12,12 +12,10 @@ clo <- readr::read_csv("./Intermediate/Formatted/CLOVERFormatted.csv", col_type
 print("clo")
 pred <- vroom("./Intermediate/Formatted/PREDICTAllFormatted.csv", col_type = cols(PMID = col_double(), PublicationYear = col_double()))
 print("pred")
-globi <- vroom("./Intermediate/Formatted/GLOBIFormatted.csv", col_type = cols(PMID = col_double(), PublicationYear = col_double()))
-print("globi")
 
 if(is.numeric(clo$NCBIAccession)) {clo %<>% dplyr::mutate(NCBIAccession = as.character(NCBIAccession))}
 
-virion <- dplyr::bind_rows(clo, pred, gb, globi)
+virion <- dplyr::bind_rows(clo, pred, gb)
 #   
 # chr_cols <- names(virion[, sapply(virion, is.character)])
 # virion <- virion %>%

diff --git a/Code/04_High level VIRION checks.R b/Code/04_High level VIRION checks.R
@@ -75,7 +75,7 @@ virion %<>% dplyr::mutate(
 print("relocate")
 
 
-# This only applies to CLOVER and GLOBI, which both don't have any other internal flags
+# This only applies to CLOVER, which doesn't have any other internal flags
 virion %<>% dplyr::mutate(HostFlagID = replace_na(HostFlagID, FALSE)) 
 print("mutate1")