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.
2 answers
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!
•
written
by
Michael Dondrup
>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
your file is definitely broken!
read ?system.file
•
written
by
Michael Dondrup
As Michael mentioned stop using the system.file() command, use file() instead.
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)
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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.
Also, can you please rename the question to something like a question - the title looks awful and is giving me a headache :)
I am not receiving any output, I know I should be:
Regardless, here is the first sequence from my fasta file:
post your file, your file is empty possibly!
this is not the point, check my answer again!
Thanks, it works! I can start plotting now!