Closed ArtPoon closed 2 years ago
I can walk through the function code without the same problem:
> var.names=c("ID", "CollectionDate", "Subtype")
> var.transformations=list(as.character, as.Date, as.factor)
> sep='_'
> seqs <- alignment.ex
> # Split and transform data from headers
> split.headers <- sapply(names(seqs), function(x) {
+ strsplit(x, sep)[[1]]
+ })
> seq.info <- lapply(1:nrow(split.headers), function(i) {
+ x <- unname(split.headers[i, ])
+ x <- var.transformations[[i]](x)
+ data.table::data.table(x)
+ })
> seq.info <- dplyr::bind_cols(seq.info)
New names:
* x -> x...1
* x -> x...2
* x -> x...3
> colnames(seq.info) <- var.names
> seq.info[, "Header" := names(seqs)]
> seq.info
ID CollectionDate Subtype Header
1: KU190546.1 2011-09-27 subB KU190546.1_2011-09-27_subB
2: KU190384.1 2010-02-23 subB KU190384.1_2010-02-23_subB
3: KU190294.1 2009-07-06 subB KU190294.1_2009-07-06_subB
4: KU190419.1 2010-06-15 subB KU190419.1_2010-06-15_subB
5: KU190347.1 2009-11-25 subB KU190347.1_2009-11-25_subB
6: KU190221.1 2009-01-06 subB KU190221.1_2009-01-06_subB
7: KU190698.1 2012-10-18 subB KU190698.1_2012-10-18_subB
8: KU190731.1 2013-01-02 subB KU190731.1_2013-01-02_subB
9: KU190643.1 2012-04-09 subB KU190643.1_2012-04-09_subB
10: KU190710.1 2012-11-15 subB KU190710.1_2012-11-15_subB
Problem resolved by ditching the data.table :=
syntax
diff --git a/R/sequence.setup.R b/R/sequence.setup.R
index 74fac1b..ece98c5 100644
--- a/R/sequence.setup.R
+++ b/R/sequence.setup.R
@@ -46,8 +46,9 @@ pull.headers <- function(seqs, var.names, var.transformations =
list(), sep = "_
seq.info <- dplyr::bind_cols(seq.info)
colnames(seq.info) <- var.names
-
- seq.info[, "Header" := names(seqs)]
-
+
+ seq.info$Header <- names(seqs)
+ #seq.info[, "Header" := names(seqs)]
+
return(seq.info)
}
To reproduce (using commit 46fc1baa019960f052eabed6f5406db2a258c2eb):