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Thread Tools |
05-24-2012, 04:42 AM
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#1 |
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Senior Member
Location: Stuttgart, Germany Join Date: Apr 2010
Posts: 192
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Parse Labels from newick tree
Hey there,
I am searching for script which extract the node labels from a given newick String. Is there any tool available at the internet, or maybe someone of you guys can help me... Best, Phil |
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05-24-2012, 06:14 AM
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#2 |
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Peter (Biopython etc)
Location: Dundee, Scotland, UK Join Date: Jul 2009
Posts: 1,543
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There are several options available - which programing language are you happiest with? If Python, then Biopython includes a Newick parser.
Also it would help if you could clarify exactly what you want to get out - just a list of the node labels, throwing away the tree structure? |
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05-24-2012, 07:19 AM
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#3 |
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Senior Member
Location: Stuttgart, Germany Join Date: Apr 2010
Posts: 192
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I just want to have the labels. Tree structure can be thrown away... Python is fine...
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05-24-2012, 07:24 AM
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#4 |
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Peter (Biopython etc)
Location: Dundee, Scotland, UK Join Date: Jul 2009
Posts: 1,543
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If there are internal node labels, do you want the terminal (leaf) names only?
e.g. Using Biopython Code:
from Bio import Phylo
tree = Phylo.read("int_node_labels.nwk", "newick")
for leaf in tree.get_terminals(): print leaf.name
Last edited by maubp; 05-24-2012 at 07:27 AM. Reason: Adding script |
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05-24-2012, 08:22 AM
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#5 |
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Senior Member
Location: Stuttgart, Germany Join Date: Apr 2010
Posts: 192
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Internal as well would be great...
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05-24-2012, 08:40 AM
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#6 | |
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Peter (Biopython etc)
Location: Dundee, Scotland, UK Join Date: Jul 2009
Posts: 1,543
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Quote:
Code:
from Bio import Phylo
tree = Phylo.read("int_node_labels.nwk", "newick")
for node in tree.get_nonterminals(): print node.name
Code:
from Bio import Phylo
tree = Phylo.read("int_node_labels.nwk", "newick")
for node in tree.find_clades():
#Don't print anything if there is no name
if node.name:
print node.name
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05-24-2012, 11:19 AM
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#7 |
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Senior Member
Location: Stuttgart, Germany Join Date: Apr 2010
Posts: 192
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thanks alot!
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