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" <[EMAIL PROTECTED]> To: "Hiroyuki Hashimoto" <[EMAIL PROTECTED]> Cc: <[EMAIL PROTECTED]> 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 - [EMAIL PROTECTED] > > http://biojava.org/mailman/listinfo/biojava-l > > > > > -- > BioJava Consulting LTD - Support and training for BioJava > http://www.biojava.co.uk > > _______________________________________________ > 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
