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  "id" "ali" $class  "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.