Similar to change counter notebook, but explictly iterates, rather than using Dendropy iteration. This does not make a difference to the final outcome.
In [2]:
import dendropy
import pandas as pd
In [3]:
data = pd.read_csv('../Data/PyronParityData.csv', index_col=0, header=False)
In [4]:
taxa = dendropy.TaxonSet()
mle = dendropy.Tree.get_from_path('../2598364_0', 'newick', taxon_set=taxa, preserve_underscores=True,extract_comment_metadata=True)
In [5]:
for idx, nd in enumerate(mle.leaf_iter()):
if nd.label is None:
lookup = '{}'.format(nd.taxon)
nd.label = int(data.ix[lookup])
else:
pass
In [6]:
origins = [] #changes to viviparity
reversions = [] #reversions to oviparity
total = [] #should equal 3951
childs = []
for index, node in enumerate(mle.postorder_node_iter()):
if node.parent_node is None:
pass
if float(node.label) == 0 or 1 > float(node.label) > .5:
total.append(node)
if node.parent_node is None:
pass
elif float(node.parent_node.label) < 0.05:
reversions.append(node)
foci = node.parent_node
if foci.parent_node is None:
print 'root'
elif float(node.parent_node.label) > .5:
new_foci = node.parent_node
if new_foci.parent_node is None:
pass
elif float(new_foci.parent_node.label) < 0.05:
reversions.append(new_foci)
elif float(node.parent_node.label) > .05:
new_foci = node.parent_node
if new_foci.parent_node is None:
pass
elif float(new_foci.parent_node.label) < 0.05:
reversions.append(new_foci)
print len(set(reversions)), 'reversions'
print set(reversions)
818 reversions
set([<dendropy.dataobject.tree.Node object at 0xadc1e1ac>, <dendropy.dataobject.tree.Node object at 0xae15804c>, <dendropy.dataobject.tree.Node object at 0xadfb956c>, <dendropy.dataobject.tree.Node object at 0xae1c6acc>, <dendropy.dataobject.tree.Node object at 0xae0600cc>, <dendropy.dataobject.tree.Node object at 0xadc8c02c>, <dendropy.dataobject.tree.Node object at 0xadfc958c>, <dendropy.dataobject.tree.Node object at 0xae15014c>, <dendropy.dataobject.tree.Node object at 0xadb9816c>, <dendropy.dataobject.tree.Node object at 0xae06018c>, <dendropy.dataobject.tree.Node object at 0xadd581ac>, <dendropy.dataobject.tree.Node object at 0xaddc81cc>, <dendropy.dataobject.tree.Node object at 0xae1815ac>, <dendropy.dataobject.tree.Node object at 0xae406b0c>, <dendropy.dataobject.tree.Node object at 0xae15406c>, <dendropy.dataobject.tree.Node object at 0xadb9830c>, <dendropy.dataobject.tree.Node object at 0xadba170c>, <dendropy.dataobject.tree.Node object at 0xae21032c>, <dendropy.dataobject.tree.Node object at 0xadb9d5ec>, <dendropy.dataobject.tree.Node object at 0xae15036c>, <dendropy.dataobject.tree.Node object at 0xae15838c>, <dendropy.dataobject.tree.Node object at 0xadc16b4c>, <dendropy.dataobject.tree.Node object at 0xadc703ac>, <dendropy.dataobject.tree.Node object at 0xae0603ec>, <dendropy.dataobject.tree.Node object at 0xaddc842c>, <dendropy.dataobject.tree.Node object at 0xadc675ec>, <dendropy.dataobject.tree.Node object at 0xae21048c>, <dendropy.dataobject.tree.Node object at 0xadb7c0cc>, <dendropy.dataobject.tree.Node object at 0xae24162c>, <dendropy.dataobject.tree.Node object at 0xae1584ec>, <dendropy.dataobject.tree.Node object at 0xadc7050c>, <dendropy.dataobject.tree.Node object at 0xae06052c>, <dendropy.dataobject.tree.Node object at 0xae26054c>, <dendropy.dataobject.tree.Node object at 0xadc8c0ec>, <dendropy.dataobject.tree.Node object at 0xadb9856c>, <dendropy.dataobject.tree.Node object at 0xadc8964c>, 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<dendropy.dataobject.tree.Node object at 0xadb9d28c>, <dendropy.dataobject.tree.Node object at 0xae1c6f2c>, <dendropy.dataobject.tree.Node object at 0xadb8ef4c>, <dendropy.dataobject.tree.Node object at 0xadccaf4c>, <dendropy.dataobject.tree.Node object at 0xae406f6c>, <dendropy.dataobject.tree.Node object at 0xadcc6f8c>, <dendropy.dataobject.tree.Node object at 0xadc7c1ac>, <dendropy.dataobject.tree.Node object at 0xae2212ac>, <dendropy.dataobject.tree.Node object at 0xae276fec>, <dendropy.dataobject.tree.Node object at 0xadc5702c>, <dendropy.dataobject.tree.Node object at 0xadbbfd6c>, <dendropy.dataobject.tree.Node object at 0xae03f06c>, <dendropy.dataobject.tree.Node object at 0xadc579cc>, <dendropy.dataobject.tree.Node object at 0xadc4f0cc>, <dendropy.dataobject.tree.Node object at 0xadec9e4c>, <dendropy.dataobject.tree.Node object at 0xadc6710c>, <dendropy.dataobject.tree.Node object at 0xae03f12c>, <dendropy.dataobject.tree.Node object at 0xadd912ec>, <dendropy.dataobject.tree.Node object at 0xadb571ac>, <dendropy.dataobject.tree.Node object at 0xae1cf1cc>, <dendropy.dataobject.tree.Node object at 0xadc5fdac>, <dendropy.dataobject.tree.Node object at 0xadba5aac>, <dendropy.dataobject.tree.Node object at 0xadbbf22c>, <dendropy.dataobject.tree.Node object at 0xadc1e86c>, <dendropy.dataobject.tree.Node object at 0xadc4f26c>, <dendropy.dataobject.tree.Node object at 0xadc845ec>, <dendropy.dataobject.tree.Node object at 0xadc572ec>, <dendropy.dataobject.tree.Node object at 0xae1cf36c>, <dendropy.dataobject.tree.Node object at 0xadbb134c>, <dendropy.dataobject.tree.Node object at 0xadc673ac>, <dendropy.dataobject.tree.Node object at 0xae0373cc>, <dendropy.dataobject.tree.Node object at 0xae4068ac>, <dendropy.dataobject.tree.Node object at 0xaddf936c>, <dendropy.dataobject.tree.Node object at 0xae03f48c>, <dendropy.dataobject.tree.Node object at 0xadb574ac>, <dendropy.dataobject.tree.Node object at 0xadc4f4cc>, <dendropy.dataobject.tree.Node object at 0xadc674ec>, <dendropy.dataobject.tree.Node object at 0xadebf50c>, <dendropy.dataobject.tree.Node object at 0xade5138c>, <dendropy.dataobject.tree.Node object at 0xae03752c>, <dendropy.dataobject.tree.Node object at 0xae08a8ec>, <dendropy.dataobject.tree.Node object at 0xadbc7e4c>, <dendropy.dataobject.tree.Node object at 0xadc4f5cc>, <dendropy.dataobject.tree.Node object at 0xadbb93ac>, <dendropy.dataobject.tree.Node object at 0xae0375ec>, <dendropy.dataobject.tree.Node object at 0xadc5764c>, <dendropy.dataobject.tree.Node object at 0xadbbfe6c>, <dendropy.dataobject.tree.Node object at 0xadebf66c>, <dendropy.dataobject.tree.Node object at 0xae03f6ac>, <dendropy.dataobject.tree.Node object at 0xadb576cc>, <dendropy.dataobject.tree.Node object at 0xadd99f4c>, <dendropy.dataobject.tree.Node object at 0xae0576ec>, <dendropy.dataobject.tree.Node object at 0xae02f70c>, <dendropy.dataobject.tree.Node object at 0xadc8970c>, <dendropy.dataobject.tree.Node object at 0xadebf72c>, <dendropy.dataobject.tree.Node object at 0xae03774c>, <dendropy.dataobject.tree.Node object at 0xadbb1ccc>, <dendropy.dataobject.tree.Node object at 0xadd996cc>, <dendropy.dataobject.tree.Node object at 0xae1cf7ac>, <dendropy.dataobject.tree.Node object at 0xae03cb8c>, <dendropy.dataobject.tree.Node object at 0xaddf3eac>, <dendropy.dataobject.tree.Node object at 0xadb4f7ec>, <dendropy.dataobject.tree.Node object at 0xadb524cc>, <dendropy.dataobject.tree.Node object at 0xadc8140c>, <dendropy.dataobject.tree.Node object at 0xadde782c>, <dendropy.dataobject.tree.Node object at 0xae05784c>, <dendropy.dataobject.tree.Node object at 0xadc1a96c>, <dendropy.dataobject.tree.Node object at 0xadf5208c>, <dendropy.dataobject.tree.Node object at 0xadc5f88c>, <dendropy.dataobject.tree.Node object at 0xadbbf8cc>, <dendropy.dataobject.tree.Node object at 0xadb578ec>, <dendropy.dataobject.tree.Node object at 0xae03794c>, <dendropy.dataobject.tree.Node object at 0xadde798c>, <dendropy.dataobject.tree.Node object at 0xae18144c>, <dendropy.dataobject.tree.Node object at 0xadbd9c0c>, <dendropy.dataobject.tree.Node object at 0xae1cf9cc>, <dendropy.dataobject.tree.Node object at 0xae03fa0c>, <dendropy.dataobject.tree.Node object at 0xadde7a4c>, <dendropy.dataobject.tree.Node object at 0xae02fa6c>, <dendropy.dataobject.tree.Node object at 0xadebfa8c>, <dendropy.dataobject.tree.Node object at 0xae037aac>, <dendropy.dataobject.tree.Node object at 0xadc67acc>, <dendropy.dataobject.tree.Node object at 0xadc4faec>, <dendropy.dataobject.tree.Node object at 0xadbb9e4c>, <dendropy.dataobject.tree.Node object at 0xadec948c>, <dendropy.dataobject.tree.Node object at 0xae1cfb2c>, <dendropy.dataobject.tree.Node object at 0xae03fb6c>, <dendropy.dataobject.tree.Node object at 0xadf6ff4c>, <dendropy.dataobject.tree.Node object at 0xae1cfbec>, <dendropy.dataobject.tree.Node object at 0xadc5fc0c>, <dendropy.dataobject.tree.Node object at 0xae03fc2c>, <dendropy.dataobject.tree.Node object at 0xadc4fc4c>, <dendropy.dataobject.tree.Node object at 0xadb57c8c>, <dendropy.dataobject.tree.Node object at 0xadc814cc>, <dendropy.dataobject.tree.Node object at 0xadebfcac>, <dendropy.dataobject.tree.Node object at 0xae037cec>, <dendropy.dataobject.tree.Node object at 0xadc6c06c>, <dendropy.dataobject.tree.Node object at 0xae02fd0c>, <dendropy.dataobject.tree.Node object at 0xadc8c52c>, <dendropy.dataobject.tree.Node object at 0xadfd94ec>, <dendropy.dataobject.tree.Node object at 0xae057d6c>, <dendropy.dataobject.tree.Node object at 0xae286a4c>, <dendropy.dataobject.tree.Node object at 0xadde7dac>, <dendropy.dataobject.tree.Node object at 0xadc57dec>, <dendropy.dataobject.tree.Node object at 0xae02fe0c>, <dendropy.dataobject.tree.Node object at 0xadc812ac>, <dendropy.dataobject.tree.Node object at 0xadc67e4c>, <dendropy.dataobject.tree.Node object at 0xadc4fe6c>, <dendropy.dataobject.tree.Node object at 0xadde7fcc>, <dendropy.dataobject.tree.Node object at 0xadc5ff0c>, <dendropy.dataobject.tree.Node object at 0xadb4ff2c>, <dendropy.dataobject.tree.Node object at 0xadc2f26c>, <dendropy.dataobject.tree.Node object at 0xae1cff4c>, <dendropy.dataobject.tree.Node object at 0xadbb9acc>, <dendropy.dataobject.tree.Node object at 0xae057fcc>, <dendropy.dataobject.tree.Node object at 0xadbc7fec>])
In [34]:
origins = [] #changes to viviparity
for index, node in enumerate(mle.postorder_node_iter()):
if node.parent_node is None:
pass
if float(node.label) == 1 or 0 < float(node.label) < .05:
total.append(node)
if node.parent_node is None:
pass
elif float(node.parent_node.label) > 0.95:
origins.append(node)
foci = node.parent_node
if foci.parent_node is None:
print 'root'
elif float(node.parent_node.label) > .5:
new_foci = node.parent_node
if new_foci.parent_node is None:
pass
elif float(new_foci.parent_node.label) > 0.95:
origins.append(new_foci)
elif float(node.parent_node.label) > .95:
new_foci = node.parent_node
if new_foci.parent_node is None:
pass
elif float(new_foci.parent_node.label) > 0.95:
origins.append(new_foci)
print len(set(origins)), 'reversions'
print set(origins)
31 reversions
set([<dendropy.dataobject.tree.Node object at 0xad25880c>, <dendropy.dataobject.tree.Node object at 0xad7300ac>, <dendropy.dataobject.tree.Node object at 0xad61f90c>, <dendropy.dataobject.tree.Node object at 0xad3e058c>, <dendropy.dataobject.tree.Node object at 0xad8b792c>, <dendropy.dataobject.tree.Node object at 0xad2e610c>, <dendropy.dataobject.tree.Node object at 0xad2eb9cc>, <dendropy.dataobject.tree.Node object at 0xad8aa9ec>, <dendropy.dataobject.tree.Node object at 0xad209f0c>, <dendropy.dataobject.tree.Node object at 0xad68226c>, <dendropy.dataobject.tree.Node object at 0xad50128c>, <dendropy.dataobject.tree.Node object at 0xad4ab2ec>, <dendropy.dataobject.tree.Node object at 0xad850b2c>, <dendropy.dataobject.tree.Node object at 0xad89134c>, <dendropy.dataobject.tree.Node object at 0xad97f38c>, <dendropy.dataobject.tree.Node object at 0xad657b4c>, <dendropy.dataobject.tree.Node object at 0xad2753ec>, <dendropy.dataobject.tree.Node object at 0xad89144c>, <dendropy.dataobject.tree.Node object at 0xad3c44ac>, <dendropy.dataobject.tree.Node object at 0xad7f3d0c>, <dendropy.dataobject.tree.Node object at 0xad823d8c>, <dendropy.dataobject.tree.Node object at 0xad45e5cc>, <dendropy.dataobject.tree.Node object at 0xadaa0d0c>, <dendropy.dataobject.tree.Node object at 0xad64f26c>, <dendropy.dataobject.tree.Node object at 0xad3c0e6c>, <dendropy.dataobject.tree.Node object at 0xad4ab68c>, <dendropy.dataobject.tree.Node object at 0xad299eec>, <dendropy.dataobject.tree.Node object at 0xad32870c>, <dendropy.dataobject.tree.Node object at 0xad713f2c>, <dendropy.dataobject.tree.Node object at 0xad777f6c>, <dendropy.dataobject.tree.Node object at 0xada9458c>])
In [32]:
print len(childs)
0
In [73]:
In [ ]:
Content source: wrightaprilm/squamates
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