[Biopython] convert to interleaved nexus

[Peter Cock]

On Wed, Mar 27, 2013 at 11:52 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Wed, Mar 27, 2013 at 12:07 AM, natassa <natassa_g_2000 at yahoo.com> wrote:
>> Hi Peter,
>> There is a single call to write_nexus_data within the call, the second one
>> is quoted out. But it is within an if block-do you mean this is incorrect?
>
> If your alignment had 100 sequences, and the write_nexus_data call
> was inside the loop, it would be called 100 times. It should be outside
> the loop and called once only.
>
>> I can't really tell if there is a specific need for interleaved versus
>> sequential nexus, I use the file for a MrBayes analysis and the error
>> message i got when running it with a sequential nexus had  something to do
>> with max characters per line , similarly to what was discussed here:
>> http://biopython.org/pipermail/biopython-dev/2010-December/008480.html
>> I thus decided to go for an interleaved format.
>
> If your sequences are very long then yes, in order to use MrBayes
> is does seem you must use interleaved NEXUS format.
>
>> But it would be good if NexusIO supports more formats or in general, that
>> the functionalities of the write_nexus_data were more easily accessible
>> compared to the 'workaround' that I did here. I am not a biopython expert to
>> assess this though :-)
>> Thanks,
>> Natassa
>
> How about we make AlignIO default to writing interleaved Nexus if the
> sequences are very long (say over 1000 bases)? That way for small
> alignments we continue to produce non-interleaved Nexus as now
> (which has proved reliable) and automatically interleave when is it
> more likely that parsers with fixed buffers like MrBayes would fail.
>
> Peter

Ha! - it looks like I suggested this before, but the conversation died:
http://biopython.org/pipermail/biopython-dev/2010-December/008487.html

CC'ing Cymon again ;)

Peter