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Modelling viral latency within host with Kernel ABC
This project forked from brj1/latency-model
Modelling viral latency within host with Kernel ABC
Importing issue from PoonLab/PoonLab#15
Because rcolgem doesn't annotate coalescent tree simulations with state transitions (deme migrations), I am using MASTER to simulate trees under the simple Rong-Perelson model. As of commit 7c950db, the NEXUS output looks like what I expect. However, I can't parse this output with either FigTree or BioPython.
BioPython throws the following exception:
>>> tree = Phylo.read('RPTree_output.nexus', 'nexus')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 63, in read
tree = next(tree_gen)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 51, in parse
for tree in getattr(supported_formats[format], 'parse')(fp, **kwargs):
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Phylo/NexusIO.py", line 38, in parse
nex = Nexus.Nexus(handle)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Nexus/Nexus.py", line 604, in __init__
self.read(input)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Nexus/Nexus.py", line 655, in read
self._parse_nexus_block(title, contents)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Nexus/Nexus.py", line 696, in _parse_nexus_block
getattr(self, '_' + line.command)(line.options)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Nexus/Nexus.py", line 1085, in _tree
tree=opts.rest().strip())
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Nexus/Trees.py", line 70, in __init__
subtree_info, base_info = self._parse(tree)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Nexus/Trees.py", line 112, in _parse
subclades = [self._parse(subtree) for subtree in subtrees]
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Nexus/Trees.py", line 97, in _parse
val = self._get_values(tree[closing + 1:])
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Nexus/Trees.py", line 164, in _get_values
% (NODECOMMENT_START, NODECOMMENT_END))
Bio.Nexus.Trees.TreeError: Error in tree description: Found [& without matching ]
We want to start out with the same default parameters as the original paper. Refer to rong-perelson.R
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