[Biopython] Bio.Phylo: writing newick trees with internal node names
Tanya Golubchik
golubchi at stats.ox.ac.uk
Wed Mar 21 10:12:27 UTC 2012
Hi Eric,
It works in Biopython 1.59; I was using 1.58 originally. So problem solved.
There's a few other strange things in Phylo that I can't work out,
though -- for instance, what happens to 'PhyloXML.Other' attributes -- I
can write these on the tree, and save the tree, but it can't be
re-opened because the parser rejects it as improperly formatted. The
documentation is a bit vague on this; in particular, passing None to
'attributes' when creating Phylo.Other objects fails, while passing an
empty dictionary works... what is meant to be in 'attributes' when
creating an Other object?
Also, the 'is_aligned' sequence property disappears when a tree is saved
in phyloxml format and then read back using Phylo.read:
>>> print tree
Phylogeny(rooted=True, branch_length_unit='SNV')
Clade(branch_length=0.0, name='N1')
Clade(branch_length=0.0, name='C00000761')
BranchColor(blue=0, green=128, red=0)
Sequence(type='dna')
MolSeq(value='CCTTTCTATGTTCTGGACTGACGTTAAACGA',
is_aligned=True)
Clade(branch_length=0.0, name='C00000763')
BranchColor(blue=0, green=0, red=255)
Sequence(type='dna')
MolSeq(value='CCTTTcTATGTtCTGGACTGACGTTAAACGA',
is_aligned=True)
>>> Phylo.write(tree, myfile, 'phyloxml')
1
>>> tree2 = Phylo.read(myfile, 'phyloxml')
>>> print tree2
Phylogeny(rooted=True, branch_length_unit='SNV')
Clade(branch_length=0.0, name='N1')
Clade(branch_length=0.0, name='C00000761')
BranchColor(blue=0, green=128, red=0)
Sequence(type='dna')
MolSeq(value='CCTTTCTATGTTCTGGACTGACGTTAAACGA')
Clade(branch_length=0.0, name='C00000763')
BranchColor(blue=0, green=0, red=255)
Sequence(type='dna')
MolSeq(value='CCTTTcTATGTtCTGGACTGACGTTAAACGA')
Cheers
Tanya
On 20/03/12 22:11, Eric Talevich wrote:
> Hi Tanya,
>
> In case you haven't solved this yet, could you post some small portion
> of the Newick tree you're working with? It's possible that your tree is
> oddly formatted, and the Newick parser isn't picking up the internal
> node labels in the first place.
>
> In the current version of Biopython (1.59), this seems to work fine:
>
> from Bio import Phylo
> # Example file from our test suite
> tree = Phylo.read("Tests/Nexus/int_node_labels.nwk", "newick")
> # Print to the console
> print tree.format("newick")
> # To write the tree to a file, this is preferred:
> Phylo.write(tree, "my_new_file.nwk", "newick")
>
>
> Cheers,
> Eric
>
>
> On Fri, Mar 16, 2012 at 8:13 AM, Tanya Golubchik
> <golubchi at stats.ox.ac.uk <mailto:golubchi at stats.ox.ac.uk>> wrote:
>
> Dear all,
>
> I may be missing something in the documentation, but I can't seem to
> figure out how to write newick trees with internal node names (preserved
> as plain text). I think in some versions of Bio.Phylo a call to
> tree.format('newick') accomplished this by default, but currently I
> can't replicate this behaviour and get a tree with unnamed internal
> nodes.
>
> Any pointers would be appreciated!
>
> Thanks
> Tanya
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