NCBIAccession collapse + vroom patch

Removed the step from the PREDICT pipeline that collapses the accessions, and then added it at the very end of the pipeline for unique-otherwise records. Also added col_type specification for two very sparse columns that seem to get read as logical instead of double by vroom, leading to the loss of PMID and PublicationYear in the final copy. This is something users also need to be wary of when they read the data in.

Code/02_2a_Digest PREDICT.R

@@ -21,9 +21,8 @@ predict.raw %>%
          Host = `Species Scientific Name Based on Field Morphology`,
          Accession = `Genbank #`) %>%
 
-
-  group_by_at(vars(-Accession)) %>% 
-  summarize(Accession = str_c(Accession, collapse = ", ")) %>%
+  # group_by_at(vars(-Accession)) %>% 
+  # summarize(Accession = str_c(Accession, collapse = ", ")) %>%
   unique() %>%  
 
   # The below step deals with flagged host names and "cf." names equally

Code/02_2c_Digest PREDICT PCR.R

@@ -42,8 +42,8 @@ predict.raw %<>% select(Host,
   rename(NCBIAccession = "GenbankAccessionNumber") %>%
 
   # Collapse the Genbank info
-  group_by_at(vars(-NCBIAccession)) %>% 
-  summarize(NCBIAccession = str_c(NCBIAccession, collapse = ", ")) %>%
+  # group_by_at(vars(-NCBIAccession)) %>% 
+  # summarize(NCBIAccession = str_c(NCBIAccession, collapse = ", ")) %>%
   unique() %>% 
 
   # Clean up the host info

Code/03_Merge clean files.R

@@ -5,10 +5,10 @@ library(tidyverse); library(magrittr); library(vroom)
 
 source("./Code/001_TaxizeFunctions.R")
 
-gb <- vroom("Intermediate/Formatted/GenbankFormatted.csv.gz")
-clo <- read_csv("Intermediate/Formatted/CloverFormatted.csv")
-pred <- read_csv("Intermediate/Formatted/PREDICTAllFormatted.csv")
-globi <- read_csv("Intermediate/Formatted/GLOBIFormatted.csv")
+gb <- vroom("Intermediate/Formatted/GenbankFormatted.csv.gz", col_type = cols(PMID = col_double(), PublicationYear = col_double()))
+clo <- read_csv("Intermediate/Formatted/CloverFormatted.csv", col_type = cols(PMID = col_double(), PublicationYear = col_double()))
+pred <- read_csv("Intermediate/Formatted/PREDICTAllFormatted.csv", col_type = cols(PMID = col_double(), PublicationYear = col_double()))
+globi <- read_csv("Intermediate/Formatted/GLOBIFormatted.csv", col_type = cols(PMID = col_double(), PublicationYear = col_double()))
 
 if(class(clo$NCBIAccession)=='numeric') {clo %<>% mutate(NCBIAccession = as.character(NCBIAccession))}
 

Code/04_High level VIRION checks.R

@@ -1,5 +1,5 @@
 
-virion <- vroom("Intermediate/Formatted/VIRIONUnprocessed.csv.gz")
+virion <- vroom("Intermediate/Formatted/VIRIONUnprocessed.csv.gz", col_type = cols(PMID = col_double(), PublicationYear = col_double()))
 
 # # Is there anything that's not vertebrate in here?
 # 
@@ -76,4 +76,8 @@ virion %<>% select(-c(HostSynonyms))
 virion %<>% distinct()
 virion %<>% mutate(across(everything(), ~replace_na(.x, '')))
 
+virion %<>% 
+  group_by_at(vars(-NCBIAccession)) %>% 
+  summarize(NCBIAccession = str_c(NCBIAccession, collapse = ", "))
+
 vroom_write(virion, "Virion/Virion.csv.gz")

Code/05_Dissolve VIRION.R

@@ -5,7 +5,7 @@ library(magrittr)
 library(tidyverse)
 library(vroom)
 
-virion <- vroom("Virion/Virion.csv.gz")
+virion <- vroom("Virion/Virion.csv.gz", col_type = cols(PMID = col_double(), PublicationYear = col_double()))
 
 fixer <- function(x) {toString(unique(unlist(x)))}