[BioC] A problem

[Martin Morgan]

On 08/20/2013 01:52 AM, tooba AbaC wrote:
> Dear Sir/Madam,
>
> I have a problem with "readDNAStringSet" function. I've used this function
> for a file that contains a number of sequences with FASTA format (Glycolysis
>   Gluconeogenesis - Bos taurus.txt). But this function doesn't work for
> another similar file (tca.txt).
> The error is:
> "Error in .Call2("read_fasta_in_XStringSet", efp_list, nrec, skip,
> use.names,
> reading FASTA file tca.txt: ">" expected at beginning of line 1"
>
> I'm sure about the format (both of them are FASTA)! I've checked it! The
> second file is completely similar with first one!
> My second file contains an unicode character that marks
> the byte order or the file (U+FEFF).  One of my friend investigated
> the file with the linux tool "less" which shows the ByteOrderMark. After
> removing it (e.g. "tail --bytes=+4 tca.txt > tca2.txt"; result attached)
> everything works like expected.
> What's the problem with readDNAStringSet function?

It's expecting plain ASCII characters, not UTF8 or other encoding; this is a 
very standard assumption in bioinformatics. Likely you opened your file in an 
editor that changed its encoding; don't do that, or if you do be sure to save 
the file as 'plain text'.

Martin

>
> Regards,
> Tooba Abbassi Daloii
>
>
>
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