<div dir="ltr">In that last message the class definition should be <div><br></div><div><div style="font-size:12.8000001907349px">class OrderedNexus(Nexus.Nexus):</div><div style="font-size:12.8000001907349px"> """ Subclass of Bio.Nexus.Nexus used to maintain partition order """</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px"> def __init__(self, **kwargs):</div><div style="font-size:12.8000001907349px"> Nexus.Nexus.__init__(self, **kwargs)</div><div style="font-size:12.8000001907349px"> self.charpartitions = OrderedDict() </div></div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">(i.e. with the parentheses after OrderedDict..... you always see them the second you hit "send" :)</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">David</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jun 9, 2015 at 2:17 PM, David Winter <span dir="ltr"><<a href="mailto:djwinter@asu.edu" target="_blank">djwinter@asu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Michael, <div><br></div><div>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. </div><div><br></div><div>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 </div><div><br></div><div><br></div><div>from collections import OrderedDict</div><div>from Bio.Nexus import Nexus</div><div><br></div><div><div>class OrderedNexus(Nexus.Nexus):</div><div> """ Subclass of Bio.Nexus.Nexus used to maintain partition order """</div><div><br></div><div> def __init__(self, **kwargs):</div><div> Nexus.Nexus.__init__(self, **kwargs)</div><div> self.charpartitions = OrderedDict</div></div><div><br></div><div><br></div><div><br></div><div><div>o = OrderedNexus()</div><div>n = Nexus.Nexus()</div><div> o.charpartitions</div><div>#OrderedDict()</div><div>n.charpartitions</div><div>#{}</div></div><div>dir(o) # (all the stuff you expect to see in a Nexus object)</div><div><br></div><div>I haven't had a chance to test this on the example, but hope it's some help to you.</div><div><br></div><div>David</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Tue, Jun 9, 2015 at 6:37 AM, Michael Gruenstaeudl <span dir="ltr"><<a href="mailto:mi.gruenstaeudl@gmail.com" target="_blank">mi.gruenstaeudl@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Hi all,<br>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:<br><br>>>> combined.charsets.items()[0]<br>('partition0038_rps4_CDS.nex', [36567, 36568])<br><br>>>> combined.charsets.items()[1]<br>('partition0004_trnK_CDS.nex', [36569, 36573])<br><br>>>> for i in range(0,len(combined.charsets.items())):<br>... combined.charsets.items()[i] = sorted_items[i]<br>...<br>>>> combined.charsets.items()[0]<br>('partition0038_rps4_CDS.nex', [36567, 36568])<br><br>What procedure would you recommend to maintain the input order of 'file_list' in the output file 'combined.nex'?<br><br>Thank you, Michael<div><div><div><div><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><span style="font-size:12.8px">--</span><br></div><div>Michael Gruenstaeudl (Grünstäudl), PhD</div><div>E-mail: <a href="mailto:mi.gruenstaeudl@gmail.com" target="_blank">mi.gruenstaeudl@gmail.com</a></div><div>Website: <a href="http://u.osu.edu/gruenstaeudl/" target="_blank">http://blogs.fu-berlin.de/gruenstaeudl/</a></div></div></div></div></div></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div>David Winter</div><div>Postdoctoral Research Associate</div><div>Center for Evolutionary Medicine and Informatics</div><div>The Biodesign Institute</div><div>Arizona State University</div><div><br></div><div>ph: +1 480 519 5113</div><div>w: <a href="http://www.david-winter.info" target="_blank">www.david-winter.info</a></div><div>lab: <a href="http://cartwrig.ht/lab/" target="_blank">http://cartwrig.ht/lab/</a></div><div>blog: <a href="http://sciblogs.co.nz/the-atavism" target="_blank">sciblogs.co.nz/the-atavism</a></div></div></div>
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