[Biojava-l] ParseException when using interleaved Nexus file

[David Johnson]

Hi Richard,

Forgot to say after your last mail (ages ago now), thanks for all your
help! The stuff I'm using the Nexus parser in works great now.

Cheers,
-David

2009/8/11 Richard Holland <holland at eaglegenomics.com>:
> It should already be on CruiseControl.
>
> Standards in bioinformatics are a pain - people write them to describe the
> format of files their software outputs, then the very same people then
> produce files that break those standards without any additional
> documentation or explanation. (Genbank are one of the biggest offenders!) It
> makes it very hard to write parsers, because if you stick to the official
> spec there will always be files that don't work yet people insist are still
> valid, yet without prior documented evidence of invalid files that are
> considered to be valid, it is impossible to write a parser to cater for
> them. :)
>
> cheers,
> Richard
>
> On 11 Aug 2009, at 11:12, David Johnson wrote:
>
>> Hi Richard,
>>
>> OK that's good to know... I suppose that's the problem with specifications
>> - people don't always follow them!
>>
>> But I get the impression either some people think that using
>> interleave=yes/no is standard practice, or it could be being generated by
>> some other phylo software (e.g. maybe PAUP or some other tools).
>>
>> I had a talk with my supervisor and he actually can't find the specific
>> programs that have been putting that in, but looking at a range of his Nexus
>> files, there's quite a few that seem to use put in the yes/no bits, some
>> files he received from other researchers.
>>
>> Are the modifications available in the latest automated build (on
>> CruiseControl)?
>>
>> Cheers,
>> -David
>>
>> 2009/8/11 Richard Holland <holland at eaglegenomics.com>
>> I've found the problem - "interleave=yes" is not valid according to the
>> official NEXUS format spec which the parser was written against. (Maddison
>> et al., 1997)
>>
>> Interleaved file are supposed to only include the word "interleave" - it
>> takes no parameters. Non-interleaved files shouldn't mention it at all.
>>
>> I've modified the parser to tolerate this but I'd be interested to know
>> where the invalid token came from - was it added manually, or by an existing
>> piece of publically available software?
>>
>> The modification has been made in the trunk of the biojava-live subversion
>> repository.
>>
>> cheers,
>> Richard
>>
>>