[Biojava-l] Impossible to catch Location parsing Error

[Hiroyuki Hashimoto]

Hi, Matthew.

Thank you for a reply.
I am sorry that my reply is overdue.

It is as follows that I checked;

(1) AB042240    misc_feature    134545^1
(2) AB046436    misc_feature    92619..88345
(3) AB033993    misc_feature    2636..2382
(4) AB047280    repeat_unit     11648..1676

And I got them in GenBank format, their features is deleted, except (1).
If you want to DDBJ Format, please access URL below;
http://getentry.ddbj.nig.ac.jp/getstart-e.html

Probably, you turn out that DDBJ format is almost the same as GenBank 
except for the point of GI Number. 

Regards, 

Hiroyuki

----- Original Message ----- 
From: "Matthew Pocock" <matthew_pocock@yahoo.co.uk>
To: "Hiroyuki Hashimoto" <hirohash@genes.nig.ac.jp>
Cc: <biojava-l@biojava.org>
Sent: Friday, September 20, 2002 8:17 PM
Subject: Re: [Biojava-l] Impossible to catch Location parsing Error


> Hi Hiroyuki,
> 
> The genbank parser was not designed with DDBJ in mind, so I am not
> supprised that it fails. I am suprised that you have feataures with
> backwards coordinates - I thought that genbank, embl and DDBJ had agreed
> to use the exact same feature table format, but I may be wrong here. Do
> you have the accession number for an entry that fails?
> 
> The short answer is to grab the corresponding embl or genbank entry. The
> better solution is to double-check that you have a legal entry, and if
> you do, we can make a copy of the genbank parser called DDBJFormat and
> add in the extra code necisary to handle your backwards features.
> 
> Best,
> 
> Matthew
> 
> Hiroyuki Hashimoto wrote:
> > Hello, everyone.
> > 
> > I mail BioJava-ML for the first time.
> > 
> > I'm trying to parse DDBJ Format data, which is similar to GenBank-Format.
> > 
> > The problem arose.
> > DDBJ's data contain illegal? Location of Feature, so the number of start
> > position is greater than that of end position, for example, "92619..88345".
> > BioJava's parser read out stderr message;
> > "This line could not be parsed: misc_feature    92619..88345"
> > But not throw Exception, so it is impossible to catch this error..
> > And it is ignored after that.
> > 
> > They are being caught if it carries out what, or a bug?
> > 
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> 
> 
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