One way to do this would be to create a Unicode alphabet (or ASCII
alphabet) and read the file into a Sequence of that Alphabet, create a
Distribution, compare it to the DNA/ RNA/ Protein distributions using
DistributionTools and then convert it to the correct Alphabet.
Even more ambitious would be to read the whole file to a text buffer and
guess the format and alphabet based on the usage of characters.
Anyone feel inspired to do something like this. We are always getting
emails from students looking for short projects. How about that one? My
basic minimal requirement would be that the file should not be read twice.
I/O is expensive, Memory is cheap.
- Mark
Thomas Down <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
11/13/2004 12:26 AM
To: Mark Schreiber/GP/[EMAIL PROTECTED]
cc: biojava-list <[EMAIL PROTECTED]>
Subject: Re: [Biojava-l] opening unknown fasta file
On Fri, Nov 12, 2004 at 10:01:13AM +0800,
[EMAIL PROTECTED] wrote:
>
> Bascially there is absolutely no failsafe way to know if a fasta file is
> DNA or Protein (or RNA). It's perfectly reasonable to have a short
peptide
> which contains only acg and t although it becomes very unlikely with
> longer sequences.
The real problem isn't A, C, G, or T, but the other 11 ambiguity symbols
that appear in DNA sequences. Ns are everywhere, but many of the other
ambiguities appear from time to time, too.
If we were *really* serious about alphabet-guessing (which scares me, to
be
honest), one option would be to calculate histograms of character
frequencies
in EMBL and Swissprot, and look for the closest match. I believe that
Internet Explorer takes this approach when it hits a web page without an
explicitly-specified character encoding -- it apparently works pretty
well...
Does anyone feel this serious?
Thomas.
_______________________________________________
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
_______________________________________________
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
