t: 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
>
y thoughts,
jess vermont
chicago
Universes of virtually unlimited complexity can be created in the form of
computer programs. (Joseph Weizenbaum)
From: Thomas Down <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
CC: biojava-list <[EMAIL PROTECTED]>
Subject: Re: [Biojava-l] opening unknow
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
> l
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
>
am.
- Mark
Koen van der Drift <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
11/12/2004 06:21 AM
To: biojava-list <[EMAIL PROTECTED]>
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] opening unknown fasta file
Hi,
The Bio
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
