Title: GenBank parsing problem
Hi all,
I am trying to parse a GenBank file (accession number: NT_005403) downloaded from NCBI. Using SequenceIterator to get the nextSequence gives the following output:
This line could not be parsed: aa:OTHER)
This line could not be parsed:
ED]]
> Sent: Tuesday, April 30, 2002 5:33 PM
> To: Thomas Down; Simon Foote
> Cc: [EMAIL PROTECTED]
> Subject: RE: [Biojava-l] Genbank parsing problem
>
>
> To my mind a wholey remote feature is not really a Feature in the
> biojava sense and might be best handled as a
[EMAIL PROTECTED]]
> Sent: Wednesday, 1 May 2002 3:26 a.m.
> To: Simon Foote
> Cc: [EMAIL PROTECTED]
> Subject: Re: [Biojava-l] Genbank parsing problem
>
>
> On Tue, Apr 30, 2002 at 09:12:59AM -0400, Simon Foote wrote:
> > I've recently run across a problem with p
> I've recently run across a problem with parsing of
Genbank files
> containing unbounded locations.
Our solution in the AGAVE Java library was to create a
location object in an "invalid" state when the
location was out of range or the location string was
otherwise unparseable. The location obj
On Tue, Apr 30, 2002 at 09:12:59AM -0400, Simon Foote wrote:
> I've recently run across a problem with parsing of Genbank files
> containing unbounded locations.
> Anyone have any idea what's causing it. I tried to trace it back
> through but got lost. But I think it has to do with the single
Hi Simon,
I think I've been bitten by something like this in SwissProt files
(initiation at 0?). I'll have a dig arround in the simple feature
constructor and see if it is handling fuzzies correctly.
Matthew
Simon Foote wrote:
> I've recently run across a problem with parsing of Genbank files
I've recently run across a problem with parsing of Genbank files
containing unbounded locations.
Anyone have any idea what's causing it. I tried to trace it back
through but got lost. But I think it has to do with the single <1 for
the -35_signal as shown in the example.
Thanks,
Simon Foote
