[Biopython] Maintaining partition order in concatenated nexus

[Michael Gruenstaeudl]

Hi David,
thank you for your response. However, I am not fully certain that I 
understand your suggested way forward. Is the below example what you 
meant (and if so, how would you debug it)?
Thank you, Michael


 >>> from Bio.Nexus import Nexus
 >>> import glob
 >>> file_list = glob.glob('*.nex')
 >>> file_list.sort() # Important step
 >>> nexi = [(fname, Nexus.Nexus(fname)) for fname in file_list]
 >>> from collections import OrderedDict
 >>> class OrderedNexus(Nexus.Nexus):
...   def __init__(self, **kwargs):
...     Nexus.Nexus.__init__(self, **kwargs)
...     self.charpartitions = OrderedDict()
...
 >>> nexi_ordered = [(n[0], OrderedNexus(n[1])) for n in nexi]
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
TypeError: __init__() takes exactly 1 argument (2 given)
 >>> # Would be followed by: combined = Nexus.combine(nexi_ordered)



Michael Grünstäudl (Gruenstaeudl), PhD
E-mail: mi.gruenstaeudl at gmail.com
Website: http://blogs.fu-berlin.de/gruenstaeudl/


On 06/09/2015 11:19 PM, David Winter wrote:
> In that last message the class definition should be
>
> class OrderedNexus(Nexus.Nexus):
>      """ Subclass of Bio.Nexus.Nexus used to maintain partition order """
>
>      def __init__(self, **kwargs):
>          Nexus.Nexus.__init__(self, **kwargs)
>          self.charpartitions = OrderedDict()
>
> (i.e. with the parentheses after OrderedDict..... you always see them
> the second you hit "send" :)
>
> David
>
> On Tue, Jun 9, 2015 at 2:17 PM, David Winter <djwinter at asu.edu
> <mailto:djwinter at asu.edu>> wrote:
>
>     Hi Michael,
>
>     I think this is a result of  "charpartitions" in the Nexus object
>     being a dictionary. In python dictionaries are "unordered", so you
>     don't usually get objects back out in the order they went in.
>
>     One possible workaround it to make you own class that inherits
>     everything else from Nexus but instead uses an ordered  dictionary
>     (from collections), something like
>
>
>     from collections import OrderedDict
>     from Bio.Nexus import Nexus
>
>     class OrderedNexus(Nexus.Nexus):
>          """ Subclass of Bio.Nexus.Nexus used to maintain partition
>     order """
>
>          def __init__(self, **kwargs):
>              Nexus.Nexus.__init__(self, **kwargs)
>              self.charpartitions = OrderedDict
>
>
>
>     o = OrderedNexus()
>     n = Nexus.Nexus()
>       o.charpartitions
>     #OrderedDict()
>     n.charpartitions
>     #{}
>     dir(o) # (all the stuff you expect to see in a Nexus object)
>
>     I haven't had a chance to test this on the example, but hope it's
>     some help to you.
>
>     David
>
>
>     On Tue, Jun 9, 2015 at 6:37 AM, Michael Gruenstaeudl
>     <mi.gruenstaeudl at gmail.com <mailto:mi.gruenstaeudl at gmail.com>> wrote:
>
>         Hi all,
>         like many others, I have been using the excellent example on the
>         Biopython wiki to concatenate multiple alignments into one
>         nexus-file using Biopython's Nexus.combine() function. However,
>         what if I wish to maintain the order of the nexus-partitions
>         specified in 'file_list'. While the tuple 'nexi' is still
>         ordered according to 'file_list', 'combined.charsets.items()' is
>         not. Moreover, sorting the charsets is not possible:
>
>          >>> combined.charsets.items()[0]
>         ('partition0038_rps4_CDS.nex', [36567, 36568])
>
>          >>> combined.charsets.items()[1]
>         ('partition0004_trnK_CDS.nex', [36569, 36573])
>
>          >>> for i in range(0,len(combined.charsets.items())):
>         ...     combined.charsets.items()[i] = sorted_items[i]
>         ...
>          >>> combined.charsets.items()[0]
>         ('partition0038_rps4_CDS.nex', [36567, 36568])
>
>         What procedure would you recommend to maintain the input order
>         of 'file_list' in the output file 'combined.nex'?
>
>         Thank you, Michael
>
>         --
>         Michael Gruenstaeudl (Grünstäudl), PhD
>         E-mail: mi.gruenstaeudl at gmail.com <mailto:mi.gruenstaeudl at gmail.com>
>         Website: http://blogs.fu-berlin.de/gruenstaeudl/
>         <http://u.osu.edu/gruenstaeudl/>
>
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>
>
>
>
>     --
>     David Winter
>     Postdoctoral Research Associate
>     Center for Evolutionary Medicine and Informatics
>     The Biodesign Institute
>     Arizona State University
>
>     ph: +1 480 519 5113 <tel:%2B1%20480%20519%205113>
>     w: www.david-winter.info <http://www.david-winter.info>
>     lab: http://cartwrig.ht/lab/
>     blog: sciblogs.co.nz/the-atavism <http://sciblogs.co.nz/the-atavism>
>
>
>
>
> --
> David Winter
> Postdoctoral Research Associate
> Center for Evolutionary Medicine and Informatics
> The Biodesign Institute
> Arizona State University
>
> ph: +1 480 519 5113
> w: www.david-winter.info <http://www.david-winter.info>
> lab: http://cartwrig.ht/lab/
> blog: sciblogs.co.nz/the-atavism <http://sciblogs.co.nz/the-atavism>