Move files with specific name pattern to specific subfolders - r

Question

So I would like to copy files to a specific folder based on a certain part in their name. For your overview I put my folder structure below. In the folders D1 and D2 I have multiple files (as example I put names of two files here) and the folders Brightfield and FITC. I would like to move the .TIF files to either the folder Brightfield or FITC dependent on whether the file name has brightfield in its name or FITC (see what I would like).
Current situation:
main Directory
|
|___ Experiment
├── D1
├── Brightfield
│ └── FITC
|__ 20210205_DML_3_4_D1_PM_flow__w1brightfield 100 - CAM_s3_t5.TIF
|__ 20210205_DML_3_4_D1_PM_flow__w2FITC 100- CAM_s3_t5.TIF
└── D2
├── temperature
└── weather
|__ 20210219_DML_3_4_D2_AM_flow__w1brightfield 100 - CAM_s4_t10.TIF
|__ 20210219_DML_3_4_D2_AM_flow__w2FITC 100- CAM_s4_t10.TIF
What I would like:
main Directory
|
|___ Experiment
├── D1
├── Brightfield
|__20210205_DML_3_4_D1_PM_flow__w1brightfield 100 - CAM_s3_t5.TIF
└── FITC
|__ 20210205_DML_3_4_D1_PM_flow__w2FITC 100- CAM_s3_t5.TIF
├── D2
├── Brightfield
|__20210219_DML_3_4_D2_AM_flow__w1brightfield 100 - CAM_s4_t10.TIF
└── FITC
|__20210219_DML_3_4_D2_AM_flow__w2FITC 100- CAM_s4_t10.TIF
In another question asked on stackoverflow I found a code that I thought I could adjust to my situation, but I get an error that says: Error in mapply(FUN = function (path, showWarnings = TRUE, recursive = FALSE, : zero-length inputs cannot be mixed with those of non-zero length. Apparently the list that needs to be formed (in parts) only shows NA. The code that I used is below:
files <- c("20210205_DML_3_4_D0_PM_flow__w1brightfield 100 - CAM_s3_t5.TIF", "20210205_DML_3_4_D0_PM_flow__w2FITC 100- CAM_s3_t5.TIF",
"20210219_DML_3_4_D1_AM_flow__w1brightfield 100 - CAM_s4_t10.TIF", "20210219_DML_3_4_D1_AM_flow__w2FITC 100- CAM_s4_t10.TIF")
# write some temp (empty) files for copying
for (f in files) writeLines(character(0), f)
parts <- strcapture(".*_(D[01])_*_([brightfield]|[FITC])_.*", files, list(d="", tw=""))
parts
# d tw
# 1 D0 Brightfield
# 2 D0 FITC
# 3 D1 Brightfield
# 4 D1 FITC
dirs <- do.call(file.path, parts[complete.cases(parts),])
dirs
# [1] "D0/Brightfield" "D0/FITC" "D1/Brightfield" "D1/FITCr"
### pre-condition, only files, no dir-structure
list.files(".", pattern = "D[0-9]", full.names = TRUE, recursive = TRUE)
# [1] "./20210205_DML_3_4_D0_PM_flow__w1brightfield 100 - CAM_s3_t5.TIF" "./"20210205_DML_3_4_D0_PM_flow__w2FITC 100- CAM_s3_t5.TIF"
### create dirs, move files
Vectorize(dir.create)(unique(dirs), recursive = TRUE) # creates both D0 and D0/Brightfield, ...
# D0/Brightfield D0/FITC D1/Brightfield D1/FITC
# TRUE TRUE TRUE TRUE
file.rename(files, file.path(dirs, files))
# [1] TRUE TRUE TRUE TRUE
### post-condition, files in the correct locations
list.files(".", pattern = "D[0-9]", full.names = TRUE, recursive = TRUE)
Where is it going wrong?

Answer 1

You are doing the parts <- bit wrong, it should be like so:
parts <- strcapture(".*_(D[01])_.*(brightfield|FITC).*", files, list(d="", tw=""))
parts
Output:
> parts
d tw
1 D0 brightfield
2 D0 FITC
3 D1 brightfield
4 D1 FITC
There were a couple of errors:
you forgot a . in _*_ , correct should be _.*_.
Don't put [] around the words brightfield and FITS, that's not how you use [].
there aren't underscores around brightfield or FITC in your filenames. So don't put underscores around them in your regular expression.
May I recommend reading up on an introduction article or a tutorial? It does not take much to learn what you need to overcome your problems here.