Problem with seqinr::load.fasta "The specified file does not exist."

Question

[carroll]

Hi everyone,

I'm having troubles importing a FASTA file using load.fasta() from the kodonz package. I installed and loaded the package, then:

library("kodonz")
library("seqinr") # load.fasta 

ac <- load.fasta(file = "https://fungidb.org/common/downloads/release-47/Acandida2VRR/fasta/data/FungiDB-47_Acandida2VRR_AnnotatedCDSs.fasta")

And got the following error message:

The specified file does not exist. 
Please check the file name and try again.

What might be the problem? I do not get this error when I use read.fasta(). I'd be very grateful for any suggestions, I'm just a beginner :)

[GenoMax]

It is less likely that the package supports reading a file over the web using http protocol. Have you tried to save the file locally first? If you put that link is a browser window, you should be prompted to save the file locally.

[carroll]

Thank you for you reply! I tried it and it didn't work (a different file, but still the same issue and error message):

   pi <- load.fasta(file="C:/Users/Tomasz.x230/Desktop/FungiDB-47_PinfestansT30-4_AnnotatedCDSs")

In fact, the file seems not to exist:

> file.exists("C:/Users/Tomasz.x230/Desktop/FungiDB-47_PinfestansT30-4_AnnotatedCDSs")
[1] FALSE

I think this is the same problem as in https://community.rstudio.com/t/rstudio-on-windows-10-while-saving-any-type-of-file-i-get-file-not-found-and-permissions-are-not-the-issue/29705 but cannot fix it at the moment.

[ATpoint]

The .fasta suffix is missing.

Answer 1

[ATpoint]

If you check the source code of that function you see that it checks file existence with file.exists() so it must be a file on a drive, you cannot stream this. Simply download to disk and then load from there as genomax suggests.

library(seqinr)

# download the file
download.file(url = "https://fungidb.org/common/downloads/release-47/Acandida2VRR/fasta/data/FungiDB-47_Acandida2VRR_AnnotatedCDSs.fasta", 
              destfile = "FungiDB-47_Acandida2VRR_AnnotatedCDSs.fasta")

# check if the file exists
file.exists("FungiDB-47_Acandida2VRR_AnnotatedCDSs.fasta")
# [1] TRUE

# import
myFasta <- read.fasta("FungiDB-47_Acandida2VRR_AnnotatedCDSs.fasta")

# check if it exists in R
exists("myFasta")
# [1] TRUE