maybe is a naive question, I downloaded a bunch of assemblies for different organisms with the following structure;
-Parent_folder
--Genus_species_1
---genome_filename_1
---genome_filename_2
---genome_filename_n
--Genus_species_2
---genome_filename_1
---genome_filename_2
---genome_filename_n
--Genus_species_N
---genome_filename_1
---genome_filename_2
---genome_filename_n
I would like to make a table, with one column with the species name and a second column with the filename of the assembly. Something like this;
colum1 | column2
Genus_species_1 | genome_filename_1
Genus_species_1 | genome_filename_2
Genus_species_1 | genome_filename_n
Genus_species_2 | genome_filename_1
Genus_species_2 | genome_filename_2
Genus_species_2 | genome_filename_n
Genus_species_N | genome_filename_1
Genus_species_N | genome_filename_2
Genus_species_N | genome_filename_n
I tried many things, and I don't know what it's wrong whit this code;
#listing the folders containing different number of genomes;
folder_list<- list.dirs(".", full.names = FALSE)
#Remove the parent folder;
folder_list<- folder_list[-1]
#Creating two vectors to populate with the genome filename and another with the species name(same as folder name);
genomes<-NULL
species<- NULL
#Generate a loop to populate;
for (dir in 1:length(folder_list)){
files<- as.vector(list.files(file.path(WD, dir))) #Vector containing all the genome filenames
genomes<- c(genomes, files) #add the one before to the genomes vector
#next, create a vector with the number of the folder(which is the species) and repeat it as much as the number of genomes;
directories<-rep(dir, length(list.files(file.path(WD, dir))))
species<- append(species, directories) #add it to species vector
} #end of the loop
Hope someone can help!
Thank you in advance!
I recreated the directory structure and then created a data.frame where column 1 lists all child directories and column 2 lists the files in each child directory.
First, here's the code written to replicate the directory structure.
# Create parent folder
dir.create("Parent_folder")
# Create child directories and files in one go
sample_dirnames <- seq_len(3)
sapply(sample_dirnames, function(index){
# build dir path and create
dirname <- paste0("Genus_species_", sample_dirnames[index])
dir.create(paste0("Parent_folder/",dirname))
# generate three files in the current directory
sapply(seq_len(3), function(n) {
file.create(paste0("Parent_folder/", dirname, "/genome_filename_", n, ".R"))
})
})
Using the list.files function as a starting point, use recursive = TRUE. Then pipe the output into a data.frame and separate the paths into directories and filenames. This example uses functions from the dplyr package and base functions (substring, gregexpr).
# pkg
library(tidyverse)
# build object
files <- list.files("Parent_folder/", recursive = TRUE) %>%
as.data.frame(.) %>%
rename(., "path" = .) %>%
mutate(
column1 = substring(
text = path,
first = 1,
last = as.numeric(
gregexpr(
pattern = "/",
text = path
)[1]
) - 1
),
column2 = substring(
text = path,
first = as.numeric(
gregexpr(
pattern = "/",
text = path
)[1]
) + 1
)
) %>%
select(-path)
This will print out the following object
files
# column1 column2
# 1 Genus_species_1 genome_filename_1.R
# 2 Genus_species_1 genome_filename_2.R
# 3 Genus_species_1 genome_filename_3.R
# 4 Genus_species_2 genome_filename_1.R
# 5 Genus_species_2 genome_filename_2.R
# 6 Genus_species_2 genome_filename_3.R
# 7 Genus_species_3 genome_filename_1.R
# 8 Genus_species_3 genome_filename_2.R
# 9 Genus_species_3 genome_filename_3.R