Assign string to object based on filename with multiple conditions - r

Question

I'm using some switches in my R script based on the provided data and I would like to automatize the recognition of said data. The files I'm using contain the required information in their name, I'm looking for a good way to match and assign this parts.
file names:
# Folder1:
T090_V4_plate1_S90_L001_R1_001.fastq.gz
T090_V4_plate1_S90_L001_R2_001.fastq.gz
# Folder2:
T091_V4_plate2_S1_L001_R1_001.fastq.gz
T091_V4_plate2_S1_L001_R2_001.fastq.gz
# Folder3:
TNT_2017_13_V34_plate4_S13_L001_R1_001.fastq.gz
TNT_2017_13_V34_plate4_S13_L001_R2_001.fastq.gz
TNT_2017_14_V34_plate4_S14_L001_R1_001.fastq.gz
TNT_2017_14_V34_plate4_S14_L001_R2_001.fastq.gz
the two values I would like to assign to objects are V3 or V34 to the object primerset and plate[1-4] to plate. I tried it like this:
if (length(list.files(pattern = "plate1")) > 1) {
plate <<- "plate1"
} else if (length(list.files(pattern = "plate2")) > 1) {
plate <<- "plate2"
} else if (length(list.files(pattern = "plate3")) > 1) {
plate <<- "plate3"
} else if (length(list.files(pattern = "plate4")) > 1) {
plate <<- "plate4"}
if (length(list.files(pattern = "V4")) > 1) {
primerset <<- "V4"
} else if (length(list.files(pattern = "V34")) > 1) {
primerset <<- "V34"
}
# print message based on detected values from file names
if (primerset == "V34"){
cat("sequence length is 301 bp")
} else if (primerset == "V4"){
cat("sequence length is 250 bp")
}
It works fine, but it looks complicated and easy to fail. Is there a more elegant solution? I would prefer not to load a package just for this task.
Additionally I don't know how to add a break if more than one condition is met, e.g. plate1 and plate2 in the same folder (I have the data sets separated, but just to be on the safe side).
Solution:
Based on the answers below these two versions also test if only one instance of primerset or plate is present:
filenames <- list.files()
if (length(unique(sub(".*_(plate\\d)_.*", "\\1", filenames))) == 1) {
plate <- unique(sub(".*_(plate\\d)_.*", "\\1", filenames))
}
matches = stringr::str_match(filenames, '_(V\\d+)_(plate\\d)')
if (length(unique(matches[, 2])) == 1) {
primerset = unique(matches[, 2])
}

Answer 1

In base R, we can use sub to extract specific part of the string.
primerset <- sub(".*_(V4|V34)_.*", "\\1", x)
#Or more generally
#primerset <- sub(".*_(V\\d+)_.*", "\\1", x)
plate <- sub(".*_(plate\\d)_.*", "\\1", x)
where x is vector of all the filenames
x <- c("T090_V4_plate1_S90_L001_R1_001.fastq.gz",
"T090_V4_plate1_S90_L001_R2_001.fastq.gz",
"T091_V4_plate2_S1_L001_R1_001.fastq.gz",
"T091_V4_plate2_S1_L001_R2_001.fastq.gz",
"TNT_2017_13_V34_plate4_S13_L001_R1_001.fastq.gz",
"TNT_2017_13_V34_plate4_S13_L001_R2_001.fastq.gz",
"TNT_2017_14_V34_plate4_S14_L001_R1_001.fastq.gz",
"TNT_2017_14_V34_plate4_S14_L001_R2_001.fastq.gz")

Answer 2

This calls for a regular expression. Using the {stringr} package, you would write:
matches = stringr::str_match(x, '_(V\\d+)_(plate\\d)')
primerset = matches[, 2]
plate = matches[, 3]
That is: match an underscore, followed by 'V' and a single digit, followed by underscore, followed by 'plate' and a single digit. You can extend the expression to also match the lane, mate and replicate.
Best of all, the above is vectorised so it works correctly with a vector of filenames.
Note that, either way, you should not be using <<- here (this performs global rather than local assignment and is very rarely appropriate).