Partitioning taxon sets, missing partition attribute

[Maria Izabel Cavassim Alves]

I have just been trying to follow the tutorial to set the different subpopulations:

https://pythonhosted.org/DendroPy/primer/taxa_partitions.html?highlight=taxon%20group

import dendropy

seqstr = """\

    #NEXUS

     BEGIN TAXA;

         DIMENSIONS NTAX=4;

         TAXLABELS a1 a2 b1 b2;

     END;

     BEGIN CHARACTERS;

        DIMENSIONS NCHAR=7;

        FORMAT DATATYPE=DNA MISSING=? GAP=- MATCHCHAR=.;

        MATRIX

            a1 ACCTTTG

            a2 ACCTTTG

            b1 ACCTTTG

            b2 ATCTTTG

        ;

    END

    """

seqs = dendropy.DnaCharacterMatrix.get_from_string(seqstr, 'nexus')

taxon_namespace = seqs.taxon_namespace

print(dir(taxon_namespace))

def mf(t):

    return t.label[0]

tax_parts = taxon_namespace.partition(membership_func=mf)

However, by just using the example given by the website the following error is given:

AttributeError: 'TaxonNamespace' object has no attribute 'partition'

I have printed the attributes of the variable taxon_namespace. And it follows:

['__class__', '__contains__', '__copy__', '__deepcopy__', '__delattr__', '__delitem__', '__dict__', '__doc__', '__eq__', '__format__', '__getattribute__', '__getitem__', '__hash__', '__init__', '__iter__', '__len__', '__lt__', '__module__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__reversed__', '__setattr__', '__setitem__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', '_accession_index_taxon_map', '_current_accession_count', '_format_and_write_to_stream', '_get_annotations', '_get_from', '_get_label', '_has_annotations', '_label', '_lookup_label', '_parse_and_add_from_stream', '_parse_and_create_from_stream', '_read_from', '_set_annotations', '_set_label', '_taxa', '_taxon_accession_index_map', '_taxon_bitmask_map', '_write_to', 'accession_index', 'add_taxa', 'add_taxon', 'all_taxa_bitmask', 'annotations', 'append', 'as_string', 'bitmask_as_bitstring', 'bitmask_as_newick_string', 'bitmask_taxa_list', 'clear', 'clone', 'comments', 'copy_annotations_from', 'deep_copy_annotations_from', 'description', 'discard_taxon_label', 'findall', 'get_from_path', 'get_from_stream', 'get_from_string', 'get_from_url', 'get_taxa', 'get_taxa_bitmask', 'get_taxon', 'has_annotations', 'has_taxa_labels', 'has_taxon_label', 'is_case_sensitive', 'is_mutable', 'label', 'label_taxon_map', 'labels', 'new_taxa', 'new_taxon', 'populate_memo_for_taxon_namespace_scoped_copy', 'read_from_path', 'read_from_stream', 'read_from_string', 'read_from_url', 'remove', 'remove_taxon', 'remove_taxon_label', 'require_taxon', 'reverse', 'sort', 'split_as_newick_string', 'split_as_string', 'taxa_bipartition', 'taxa_bitmask', 'taxon_bitmask', 'taxon_namespace_scoped_copy', 'write', 'write_to_path', 'write_to_stream']

There is no 'partition' attribute there truly. I was wondering if I have been doing something wrong or if the names have changed. 

Cheers.

[Jeet Sukumaran]

Unfortunately, the documentation is out of date here, reflecting a feature of DendroPy 3 that was never fully migrated to DendroPy 4. We could work on bringing it in if needed. What is your use case?

[Paul Maier]

This feature appears in recent versions (e.g. DendroPy 4.3) user manuals:

https://dendropy.readthedocs.io/en/master/primer/taxa_partitions.html

I am trying to use this feature, because it seems to be a requirement for using your tool monophyletic_partition_discordance:

https://dendropy.readthedocs.io/en/master/library/reconcile.html

How can I use this tool, if taxon_namespace.partition() no longer works? Which DendroPy version should I install? 3.0? 4.3? Working example please?

Much appreciated.

[Paul Maier]

Nevermind, figured it out. The function works with DendroPy v3.9. Code is pasted below.

Next question: Does anyone know how to create a null distribution of 's', by permuting taxa?

from collections import defaultdict

from StringIO import StringIO

import dendropy

from os import listdir

from os.path import isfile, join

import glob, os

import re

mypath = '/Users/maierpa/Desktop/CH2/bgc/infiles/haplo.EN.100_raxml/'

files = []

os.chdir(mypath)

for file in glob.glob("*.tre"):

    files.append(file)

trees = dendropy.TreeList()

for i in range(0, len(files)):

trees.read_from_path(files[i], 'newick')

for tree in range(0, len(trees)):

species_partitions = [] #list of lists to hold taxon partitions

#make a dictionary with species as keys and lists of individuals as values

tax_pop_label_map = defaultdict(list)

for i in trees[tree].taxon_set:

    newtaxa = str(i).split(' ') #Somehow the '_' is lost, and replaced with a ' '

    tax_pop_label_map[newtaxa[0]].append(i)

#convert default dict list into a list of lists

for key, value in tax_pop_label_map.iteritems():

species_partitions.append(value)

#partition the taxa into species

tps = trees[tree].taxon_set.partition(membership_lists=species_partitions)

s = dendropy.reconcile.monophyletic_partition_discordance(trees[tree], tps)

locus = re.sub("RAxML_bestTree\\.([CI]\\d+)\\.tre", "\\1", files[tree])

print(locus)

print(s)

print(" ")

---------------------------------------
Paul Maier, Ph.D. Candidate

JDP in Evolutionary Biology
San Diego State University
5500 Campanile Drive
San Diego, CA 92182
Cell: (408) 691-2169
Lab: (619) 594-0457

Email: mai...@gmail.com
www.mountainmanmaier.com
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[Paul Maier]

Nevermind! Figured that one out too:

from collections import defaultdict

from StringIO import StringIO

import dendropy

from os import listdir

from os.path import isfile, join

import glob, os

import re

import random

# Get names of all tree files in directory first

mypath = '/Users/maierpa/Desktop/CH2/bgc/infiles/haplo.EN.100_raxml/'

files = []

os.chdir(mypath)

for file in glob.glob("*.tre"):

    files.append(file)

# Read in all RAxML trees

trees = dendropy.TreeList()

for i in range(0, len(files)):

trees.read_from_path(files[i], 'newick')

f = open("SlatkinMaddisonS.txt","w+")

for tree in range(0, len(trees)):

# List of lists to hold taxon partitions

species_partitions = []

# Make a dictionary with species as keys and lists of individuals as values

tax_pop_label_map = defaultdict(list)

for i in trees[tree].taxon_set:

# Somehow the '_' is lost, and replaced with a ' '

    newtaxa = str(i).split(' ')

    tax_pop_label_map[newtaxa[0]].append(i)

# Convert default dict list into a list of lists

for key, value in tax_pop_label_map.iteritems():

species_partitions.append(value)

# Partition the taxa into species

tps = trees[tree].taxon_set.partition(membership_lists=species_partitions)

# Calculate Slatkin and Maddison's 's'

s = dendropy.reconcile.monophyletic_partition_discordance(trees[tree], tps)

# Locus name in tree file name

locus = re.sub("RAxML_bestTree\\.([CI]\\d+)\\.tre", "\\1", files[tree])

# Get all pop names so they can be randomly reassigned for permutations

pops = tax_pop_label_map.keys()

sperms = []

# Randomly permute pop assignment on tree to create null distribution

permutations = 100000

for perm in range(0,permutations):

species_partitions = []

tax_pop_label_map = defaultdict(list)

for i in trees[tree].taxon_set:

    pop_rand = random.choice(pops)

    tax_pop_label_map[pop_rand].append(i)

for key, value in tax_pop_label_map.iteritems():

species_partitions.append(value)

tps = trees[tree].taxon_set.partition(membership_lists=species_partitions)

s = dendropy.reconcile.monophyletic_partition_discordance(trees[tree], tps)

sperms.append(s)

# Calculate p-value and write locus, s, and p-value to file

pval = sum(i < s for i in sperms)/float(len(sperms))

f.write(locus + "\t" + str(s) + "\t" + str(pval) + "\n")

f.close()

---------------------------------------
Paul Maier, Ph.D. Candidate

JDP in Evolutionary Biology
San Diego State University
5500 Campanile Drive
San Diego, CA 92182
Cell: (408) 691-2169
Lab: (619) 594-0457

Email: mai...@gmail.com
www.mountainmanmaier.com
---------------------------------------