[Biojava-l] Impossible to catch Location parsing Error

Matthew Pocock matthew_pocock@yahoo.co.uk
Fri, 20 Sep 2002 12:17:07 +0100

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.



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?
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