[Biopython] An error with Concatenate nexus

[Cymon Cox]

Hi Esa,

At first glance this looks like a bug.

But given that Nexus.combine() is going to discard your codonposset
character partition anyway, you could try deleting it from the Nexus file
before combining.

Regards, Cymon

On 19 May 2011 14:02, Esa Aalto <esa.aalto at oulu.fi> wrote:

> Dear group,
>
> I'm trying to concatenate 20 nexus files with the instructions given
> here:
>
> http://www.biopython.org/wiki/Concatenate_nexus
>
> but it doesn't work:
>
> Traceback (most recent call last):
>  File "C:\Python27\concate_nexus.py", line 36, in <module>
>    nexi =  [(handle.name, Nexus.Nexus(handle)) for handle in handles]
>  File "C:\Python27\lib\site-packages\Bio\Nexus\Nexus.py", line 555, in
> __init__
>    self.read(input)
>  File "C:\Python27\lib\site-packages\Bio\Nexus\Nexus.py", line 618, in
> read
>    self._parse_nexus_block(title, contents)
>  File "C:\Python27\lib\site-packages\Bio\Nexus\Nexus.py", line 659, in
> _parse_nexus_block
>    getattr(self,'_'+line.command)(line.options)
>  File "C:\Python27\lib\site-packages\Bio\Nexus\Nexus.py", line 1021, in
> _codonposset
>    raise NexusError('Formatting Error in codonposset: %s ' % options)
> NexusError: Formatting Error in codonposset: * UNTITLED = 1: 1-577\3, 2:
> 2-578\3, 3: 3-579\3
>
> The end of the first of my nex files looks like this:
>
> BEGIN SETS;
>   TaxSet A_thaliana = 1;
>   TaxSet A_lyrata = 2;
>   TaxSet Boh = 3-32;
>   TaxSet Ice = 33-60;
>   TaxSet Ith = 61-92;
>   TaxSet Kar = 93-124;
>   TaxSet Lom = 125-156;
>   TaxSet NC = 157-196;
>   TaxSet Pl = 197-236;
>   TaxSet Sp = 237-274;
>   TaxSet Stu = 275-294;
>   TaxSet South = 3-32 197-236;
>   TaxSet North = 125-156 237-274;
>   TaxSet lyrata = 2-294;
> END;
>
> BEGIN CODONS;
>   CODONPOSSET * UNTITLED =
>      1: 1-577\3,
>      2: 2-578\3,
>      3: 3-579\3;
>   CODESET * UNTITLED = Universal: all;
> END;
>
> BEGIN CODONUSAGE;
> END;
>
> BEGIN DnaSP;
>   Genome= Diploid;
>   ChromosomalLocation= Autosome;
>   VariationType= DNA_Seq_Pol;
>   Species= ---;
>   ChromosomeName= ---;
>   GenomicPosition= 1;
>   GenomicAssembly= ---;
>   DnaSPversion= Ver. 5.10.00;
> END;
>
> Could someone tell what's wrong here? Is it my nexus files or something
> in the code?
>
> Thanks for your help!
>
> Esa Aalto
>
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