[Biojava-l] Impossible to catch Location parsing Error

[Hiroyuki Hashimoto]

Thanks, Greg.

I understood your opinion.

Then, there is one proposal, to surely be reflected in the 
following version !!

Add the following information to the error message;
Former;
"This line could not be parsed: misc_feature    92619..88345"
After an improvement, for example;
"This line could not be parsed: AB046436 misc_feature    92619..88345"
                                ^^^^^^^^
Because, when it is a file with a lot of entry, it is hard to specify 
by which entry the error occurred.

Regards,
Hiroyuki

----- Original Message ----- 
From: "Cox, Greg" <gcox@netgenics.com>
To: "'Hiroyuki Hashimoto'" <hirohash@genes.nig.ac.jp>; <biojava-l@biojava.org>
Sent: Wednesday, September 25, 2002 2:07 AM
Subject: RE: [Biojava-l] Impossible to catch Location parsing Error


> With 2-4, the version I looked at didn't have the features that couldn't be
> parsed.  
> 
> With 1, the problem is that it's a circular sequence, and 134545^1 wraps
> around.  At the boot camp two years ago, I think we decided the right thing
> to do is check the flag, and promote it to 134545^(sequencelength + 1).  My
> memory is a little hazy though, could someone check me?
> 
> The reason you aren't seeing an error is that this isn't one.  Kind of.  A
> biojava sequence is returned from case 1, and it includes all the features
> except the one it couldn't handle.  An error isn't thrown because that would
> halt execution, and the parser can function to some degree.  The philosophy
> behind this choice was that even though biojava can't handle the entire
> sequence, you might be able to work with the part it could parse.  If it's
> important to you to provide all or nothing, I believe registering a listener
> with the parser that throws an exception when anything happens will prevent
> the sequence from being created.
> 
> Greg
> 
> -----Original Message-----
> From: Hiroyuki Hashimoto [mailto:hirohash@genes.nig.ac.jp]
> Sent: Monday, September 23, 2002 8:46 PM
> To: biojava-l@biojava.org
> Subject: Re: [Biojava-l] Impossible to catch Location parsing Error
> 
> 
> 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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