How To Read A Fasta File With The Bio3D Package

Question

[laemtao]

Problem: I'm using the bio3d package in R to read a fasta file with about 4 sequences. When I try to read the fasta file, I get the error message that the '>' character cannot be found. This would mean two things to me, either the fasta file is corrupted with invisible ascii characters or the permissions on the file are wrong. I checked both conditions and I am still not able to read my file.

> foo <-system.file("~/Homology/seq_temp.fa", package="bio3d")
> aln <- read.fasta(foo)
1: attributes(aln)
2: 
Error in read.fasta(foo) : 
  read.fasta: no '>' id lines found, check file format

The example xray.fa is working correctly:

> foo <-system.file("examples/hivp_xray.fa", package="bio3d")
> aln <- read.fasta(foo)
> attributes(aln)
$names
[1] "id"  "ali"

$class
[1] "fasta"

I'm not too sure what the problem can be. Writing a fasta file (unaligned or aligned) is pretty fool proof, I have no idea what is causing this error.

Thank you in advance.

[Bio_X2Y]

Please paste the first few lines of your fasta file here, e.g. use "head -5 ~Homology/seq_temp.fa". Somebody here might spot something obviously wrong with it.

[Bio_X2Y]

Also, can you please rename the question to something like a question - the title looks awful and is giving me a headache :)

[laemtao]

I am not receiving any output, I know I should be:

head -5 ~Homology/seq_temp.fa
head - 5 ~ Homology/seq_temp.fa

[laemtao]

Regardless, here is the first sequence from my fasta file:

>gi|86159715|ref|YP_466500.1| FAD-dependent pyridine nucleotide-disulphide oxidoreductase [Anaeromyxobacter dehalogenans 2CP-C]
MRVAIIGSGPAGFYAAEALLKRTDTAVDVDMFDRLPTPFGLVRGGVAPDHQRIKAVTRVFASTAARPTFR
FLGNVRLGRDVTVDDLRRHYHQIVYATGSESDRRLGIPGEGIERCTPATVFVGWYNGHPDYRHARFDLSV
RRAAVVGNGNVAVDVARILLRTRAELERTDIAAHALEALRESQVREVYLLGRRGPAQAAFSPAELRELGT
[abridged]

[Michael]

post your file, your file is empty possibly!

[Michael]

this is not the point, check my answer again!

[laemtao]

Thanks, it works! I can start plotting now!

Answer 1

[Michael]

Use the Biostrings package functions read.DNAStringset, read.AAStringset or readFASTA instead.

Edit: Nope, you simply copy pasted from the example: try

foo <- file("~/Homology/seq_temp.fa")

system.file is only for files in the R-installation!

[laemtao]

Thank you, I was not familiar with Biostrings. I've installed it and I am receiving the following output:

[laemtao]

>moo = system.file("/Homology/seq_temp.fa", package="Biostrings")
moo = readFASTA(moo)
Error in readFASTA(moo) : no FASTA sequences found
In addition: Warning messages:
1: In readFASTA(moo) :
  use 'strip.descs=FALSE' for compatibility with old version
  of readFASTA(), or 'strip.descs=TRUE' to remove the ">"
  at the beginning of the description lines and to get
  rid of this warning (see '?readFASTA' for more details)
2: In file(file, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former

[Michael]

your file is definitely broken!

[Michael]

read ?system.file

[Istvan Albert]

As Michael mentioned stop using the system.file() command, use file() instead.

[laemtao]

Thanks, it works! I can start plotting now!

[Bio_X2Y]

That's great. Laemtao, if you are happy with the answer, please accept it by clicking the check-mark on the side. Thanks.

Answer 2

[Ana Rodrigues Grant]

The R system.file() command is the problem here. That is used in the bio3d documentation to indicate that the file ("examples/hivp_xray.fa") is somewhere in the bio3d package directory, wherever that may be in your system.

When reading your own files, all you need is the actual path:

>foo <-"~/Homology/seq_temp.fa"
>aln <- read.fasta(foo)