I am trying to rename a number of files and folders with a new name.
Example old name: corrected_original_wh_ah108090.pdf
Example new name: corrected_original_gsmp01358_108090.pdf
Example old path: Data/Test2/ARGOS/wh_ah108090/crawl/corrected_original_wh_ah108090.pdf
Example new path:Data/Test2/ARGOS/gsmp01358_108090/crawl/corrected_original_gsmp01358_108090.pdf
Example metadata:
old new
wh_ah108090 gsmp01358_108090
wh_ah108091 gsmp01359_108091
wh_ah108092 gsmp01360_108092
wh_ah108093 gsmp01361_108093
wh_ah108096 gsmp01362_108096
wh_ah108102 gsmp01363_108102
wh_ah108106 gsmp01364_108106
Code:
# Read metadata for ID's #
meta <- read.csv('Metadata.csv')
# list all file paths
pathLs <- list.files('Data/Test2/', recursive = TRUE, full.names = TRUE)
# select only files with old format on the list (for full dataset where some files already have new name)
tbl<- pathLs [!grepl("gsmp", pathLs )]
# select only files with old format on metadata
metadata<- meta[!meta$old =="",]
# function to change old names for new
fileList <- apply(metadata,1,
function(x) {
fnam <- x['old']
fnam <- as.character(unlist(fnam))
newnam <- gsub(fnam, as.character(unlist(x['new'])), tbl[grepl(fnam, tbl)])
return(newnam)})
# Create dataframe with old and new names
to <- as.character(unlist(fileList))
from <- tbl
# Use rename
file.rename(from, to)
For some reason this file rename doesn't work. Is this because I cannot rename files and directories in a path at the same time?
No loops required.
metadata <- read.table(header=T, stringsAsFactors=F, text="
old new
wh_ah108090 gsmp01358_108090
wh_ah108091 gsmp01359_108091
wh_ah108092 gsmp01360_108092
wh_ah108093 gsmp01361_108093
wh_ah108096 gsmp01362_108096
wh_ah108102 gsmp01363_108102
wh_ah108106 gsmp01364_108106")
metadata$new2 <- sprintf("gsmp%05d_%s",
1357L + seq_len(nrow(metadata)), # 1357 can be anything?
gsub("\\D", "", metadata$old))
metadata
# old new new2
# 1 wh_ah108090 gsmp01358_108090 gsmp01358_108090
# 2 wh_ah108091 gsmp01359_108091 gsmp01359_108091
# 3 wh_ah108092 gsmp01360_108092 gsmp01360_108092
# 4 wh_ah108093 gsmp01361_108093 gsmp01361_108093
# 5 wh_ah108096 gsmp01362_108096 gsmp01362_108096
# 6 wh_ah108102 gsmp01363_108102 gsmp01363_108102
# 7 wh_ah108106 gsmp01364_108106 gsmp01364_108106
file.rename(metadata$old, metadata$new2) # should do it