I'm trying to create an array in python that will contain all the pairwise distances between every pair of nodes on a phylogenetic tree. I'm currently using dendropy to do this. (I initially looked at biopython but couldn't find an option to do this). The code I have so far looks like this:
import dendropy
tree_data = []
tree = dendropy.Tree.get(path="gonno_microreact_tree.nwk",schema="newick")
pdc = tree.phylogenetic_distance_matrix()
for i, t1 in enumerate(tree.taxon_namespace[:-1]):
for t2 in tree.taxon_namespace[i+1:]:
tip_pair = {}
tip_dist_list = []
tip_pair[t1] = t2
distance = pdc(t1, t2)
tip_dist_list.append(tip_pair)
tip_dist_list.append(distance)
tree_data.append(tip_dist_list)
print tree_data
This works well except for the way it writes the tip labels. For example an entry in the tree_data list looks like this:
[{<Taxon 0x7fc4c160b090 'ERS135651'>: <Taxon 0x7fc4c160b150 'ERS135335'>}, 0.0001294946558138355]
But the tips in the newick file are just labelled ERS135651 and ERS135335 respectively. How can I get dendropy to write the array with just the original tip labels so this entry would look like this:
[{ERS135651:ERS135335}, 0.0001294946558138355]
(Also I read the dendropy documentation and I'm aware that it says to use treecalc to do this, like this:
pdc = treecalc.PatristicDistanceMatrix(tree)
But I just get an error saying the command does not exist:
AttributeError: 'module' object has no attribute 'PairisticDistanceMatrix'
)
Any suggestions for how I can get this working?
Converting the tip labels to a string converted them to the name surrounded by speech marks, e.g.:
t1 = str(t1)
print t1
Gives:
"'ERS135651'"
So using string splicing to remove the extra speech marks works to convert the tip label back to it's proper name, e.g.:
t1 = t1.replace("'","")