Thanks for your attention to Bio::NEXUS! However, this isn't an error
in Bio::NEXUS-- the files you are describing are non-standard.
According to p. 592 of the standard (Maddison, et al., 1997, Syst Biol
46: 590-621),
"The first token in a standard NEXUS file must be
#NEXUS
"
You might want to check this out with the treebase bug list instead.
But I'm not sure where the problem arises. I just checked about 8
files from TreeBASE, and I did not see this problem with any of them.
I know that TreeBASE used to give out original NEXUS files submitted
by authors, which leaves it up to the authors to ensure that the file
is valid.
I hope this response is helpful.
Arlin
On Apr 29, 2011, at 1:43 AM, TEMI VARGHESE via RT wrote:
Show quoted text> Fri Apr 29 01:43:06 2011: Request 67827 was acted upon.
> Transaction: Ticket created by var03f@csiro.au
> Queue: Bio-NEXUS
> Subject: bug report
> Broken in: (no value)
> Severity: (no value)
> Owner: Nobody
> Requestors: var03f@csiro.au
> Status: new
> Ticket <URL:
https://rt.cpan.org/Ticket/Display.html?id=67827 >
>
>
> Hi Developers
>
> Congrats on the excellent nexus module.
>
> I like to bring to your attention a minor glitch.
>
> I tried to load nexus files that started with the header:
>
> NEXUS
>
> The module failed to load the file. Format exception was thrown.
> Part of
> the error is given below.
>
> -------------------------- EXCEPTION ----------------------------
> Message: 'INPUT' does not begin with the '#NEXUS' token; it does not
> appear to be a NEXUS file. An exception of type
> Bio::NEXUS::Util::Exceptions::BadFormat was thrown. This kind of error
> happens when a bad parse or unparse format was specified. Refer to the
> Bio::NEXUS::Util::Exceptions documentation for more information.
> ------------------------- STACK TRACE ---------------------------
>
>
>
> But when I changed it by adding # to the beginning, it worked.
>
> #NEXUS
>
> Most of the files in treebase do not have # in the beginning. It
> will be
> great if you could fix this error.
>
> Thank You
> Temi
>
-------
Arlin Stoltzfus (arlin@umd.edu)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org
