Dnastringset Error Biostrings In R

Question

[Tom A]

Hello Biostars,

I am attempting to import a fasta file of sequences into R using Bioconductor's 'Biostrings' package and the 'DNAStringSet' function, but I keep getting the same error:

Error in .Call2("new_XString_from_CHARACTER", classname, x, start(solved_SEW),  : 
key 112 (char 'p') not in lookup table

My fasta file ("FileName.fa") is in the following format:

>GeneNameOne
CAGACACCCATAGATACAGATAGACAGATAGAGAAGACACCACCACACAATGA
>GeneNameTwo
CGCGACATGAACCCATGATAGACGATGAGACCCCACACACACC
...etc

Does anyone have an idea on what is going on? Thanks in advance.

[Devon Ryan]

What happens if you grep p FileName.fa?

[Tom A]

Im assuming you mean, using the Unix terminal. Nothing happens.

[Devon Ryan]

Yes, I was just curious if there actually is a 'p' in the file. Apparently not. It's useful in these cases to have a small test-case that reproduces the problem. If you can make a small enough version of that file that it can be posted somewhere easily then that'd be helpful.