Hi,
The BioJava tutorial (in anger) suggests the following code to open a
fasta file:
[snip]
// get the appropriate Alphabet
Alphabet alpha = AlphabetManager.alphabetForName(args[1]);
// get a SequenceDB of all sequences in the file
SequenceDB db = SeqIOTools.readFasta(is, alpha);
But wha
Hi Koen -
There was a method in SeqIOTools that can (mostly) guess the alphabet of a
file but it is deprecated cause there is no standard convention of file
naming. ClustalW guesses by pre-reading the the file and looking for
symbols that don't occur in DNA that are found in protein. They clai
Koen,
One thing you might try is to parse the file, grab the
accession from the first line, and use regular
expressions to identify the type of sequence.
Hope this helps,
Mark Fortner
--- Koen van der Drift <[EMAIL PROTECTED]> wrote:
> Hi,
>
> The BioJava tutorial (in anger) suggests the
>
