[Biopython] An error with Concatenate nexus
Esa Aalto
esa.aalto at oulu.fi
Thu May 19 13:02:17 UTC 2011
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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