Take sequences from fasta file and write as separate files

fasta_mover.R

# Take sequences from fasta file and write as separate files

# FUNCTION
readSqs <- function(fl) {
 all_data <- readLines(fl)
 sqs <- list()
 for(i in seq_along(all_data)) {
   bit <- all_data[[i]]
   if(grepl(pattern='^>', x=bit)) {
     nm <- sub(pattern='^>', '', x=bit)
     sqs[[nm]] <- ''
   } else {
     sqs[[nm]] <- paste0(sqs[[nm]], bit)
   }
 }
 sqs
}

# VARS
sqfl <- 'my_lovely_sequences.fasta'

# SCRIPT
sqs <- readSqs(sqfl) # read sequences from fasta
for(i in seq_along(sqs)) {  # loop through each seq
 nm <- names(sqs)[i] # get seq name
 # create file path from name, make sure it exists
 flpth <- file.path(paste0('probe', i), 'consensus')
 if(!file.exists(flpth)) {
   print(paste0('[', flpth, '] does not exist'))
    next
 }
 flpth <- file.path(flpth, paste0(nm, '.fasta'))
 if(file.exists(flpth)) {
   print(paste0('[', flpth, '] already exists'))
    next
 }
 fasta <- paste0('>', nm, '\n', sqs[[i]])  # create fasta text
 cat(fasta, file=flpth)  # write to file
}