taxon name bug
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Brian O'Meara
Jun 22, 2010, 11:43:09 AM6/22/10
to browni...@googlegroups.com
I've just found that if your taxon names start with digits (i.e.,
"14_pepper"), brownie does not parse this properly when reading
taxsets created by calling taxon names: "taxset tasty = 14_pepper" is
interpreted as "taxset tasty = 14", regardless of whatever taxon
number 14_pepper has. This becomes noticeable if the number is less
than ntax (i.e., if it can't find taxon 14 in a five taxon dataset, it
will object) but is always a problem (unless your taxon name numeric
prefix matches the order of taxa). The error has to do with how the
very old version of the NCL brownie currently uses parses names.
Passing in taxsets with numeric identifiers "taxset spicy = 1-5 7 12"
should work without problems, as should using "normal" taxon names
(i.e. "pepper").
"14_pepper"), brownie does not parse this properly when reading
taxsets created by calling taxon names: "taxset tasty = 14_pepper" is
interpreted as "taxset tasty = 14", regardless of whatever taxon
number 14_pepper has. This becomes noticeable if the number is less
than ntax (i.e., if it can't find taxon 14 in a five taxon dataset, it
will object) but is always a problem (unless your taxon name numeric
prefix matches the order of taxa). The error has to do with how the
very old version of the NCL brownie currently uses parses names.
Passing in taxsets with numeric identifiers "taxset spicy = 1-5 7 12"
should work without problems, as should using "normal" taxon names
(i.e. "pepper").
Best,
Brian
------------------------------------------------------
Brian O'Meara
http://www.brianomeara.info
Assistant Prof.
Dept. Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
jcs
Jun 23, 2010, 12:21:04 AM6/23/10
to brownie-users
How intertwined is that version with brownie? Would it be difficult
to update? just curious
On Jun 22, 11:43 am, Brian O'Meara <omeara.br...@gmail.com> wrote:
> I've just found that if your taxon names start with digits (i.e.,
> "14_pepper"), brownie does not parse this properly when reading
> taxsets created by calling taxon names: "taxset tasty = 14_pepper" is
> interpreted as "taxset tasty = 14", regardless of whatever taxon
> number 14_pepper has. This becomes noticeable if the number is less
> than ntax (i.e., if it can't find taxon 14 in a five taxon dataset, it
> will object) but is always a problem (unless your taxon name numeric
> prefix matches the order of taxa). The error has to do with how the
> very old version of the NCL brownie currently uses parses names.
> Passing in taxsets with numeric identifiers "taxset spicy = 1-5 7 12"
> should work without problems, as should using "normal" taxon names
> (i.e. "pepper").
>
> Best,
> Brian
>
> ------------------------------------------------------
> Brian O'Mearahttp://www.brianomeara.info
to update? just curious
On Jun 22, 11:43 am, Brian O'Meara <omeara.br...@gmail.com> wrote:
> I've just found that if your taxon names start with digits (i.e.,
> "14_pepper"), brownie does not parse this properly when reading
> taxsets created by calling taxon names: "taxset tasty = 14_pepper" is
> interpreted as "taxset tasty = 14", regardless of whatever taxon
> number 14_pepper has. This becomes noticeable if the number is less
> than ntax (i.e., if it can't find taxon 14 in a five taxon dataset, it
> will object) but is always a problem (unless your taxon name numeric
> prefix matches the order of taxa). The error has to do with how the
> very old version of the NCL brownie currently uses parses names.
> Passing in taxsets with numeric identifiers "taxset spicy = 1-5 7 12"
> should work without problems, as should using "normal" taxon names
> (i.e. "pepper").
>
> Best,
> Brian
>
> ------------------------------------------------------
Brian O'Meara
Jun 23, 2010, 12:54:42 AM6/23/10
to browni...@googlegroups.com
The Nexus Class Library has improved quite a bit since the one Brownie uses, but this includes several API changes, which is why I haven't updated it yet. But it'll definitely be worth doing at some point. It's also a good argument for building on existing code (i.e., to add NeXML support to Brownie, all I have to do is update the NCL, rather than write my own parser).
Brian
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________________________________________________
Brian C. O'Meara
Asst. Prof., Dept. of Ecology and Evolutionary Biology
University of Tennessee, Knoxville
http://www.brianomeara.info
865-408-TREE (8733)
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