Removing taxon with underscore

[Caleb Ji]

Hi, I'm trying to remove some taxa from newick trees, but the prune function doesn't seem to work when there are underscores in the name.

import dendropy as dp

s1 = '(A, (B, C));'

tree = dp.Tree.get(data=s1, schema="newick")

tree.prune_taxa_with_labels("A")

print(tree)

s2 = '(A_, (B, C));'

tree = dp.Tree.get(data=s2, schema="newick")

tree.prune_taxa_with_labels("A_")

print(tree)

results in:

(B,C)
(A_,(B,C))

Is there a way to remove the "A_" in s2?

Thanks,

Caleb

[Jeet Sukumaran]

As per the Newick/NEXUS standards and as stated in multiple places in
the DendroPy documentation, unless specified otherwise, "_" in labels
are parsed as spaces. So you will either need to say:

tree.prune_taxa_with_labels("A ")

or specify ``preserve_underscores=True`` when reading in the data.

> --
> You received this message because you are subscribed to the Google
> Groups "DendroPy Users" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to dendropy-user...@googlegroups.com
> <mailto:dendropy-user...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.

--



--------------------------------------
Jeet Sukumaran
--------------------------------------
jeetsu...@gmail.com
--------------------------------------
Blog/Personal Pages:
http://jeetworks.org/
GitHub Repositories:
http://github.com/jeetsukumaran
Photographs (as stream):
http://www.flickr.com/photos/jeetsukumaran/
Photographs (by galleries):
http://www.flickr.com/photos/jeetsukumaran/sets/
--------------------------------------

[Caleb Ji]

I see...still, neither of them are working for me.

import dendropy as dp
s1 = "(A_, (B, C));"
tree = dp.Tree.get(data=s1, schema="newick", preserve_underscores=False)

tree.prune_taxa_with_labels("A ")
print(tree)


s2 = "(A_, (B, C));"

tree1 = dp.Tree.get(data=s2, schema="newick", preserve_underscores=True)
tree1.prune_taxa_with_labels("A_")
print(tree1)

 gives

(A_,(B,C))
(A_,(B,C))

> <mailto:dendropy-users+unsub...@googlegroups.com>.

[Jeet Sukumaran]

The first argument should not be a single string, but a list of strings.
So, in your case, ``["A_",]`` or ``["A ",]``.

> > an email to dendropy-user...@googlegroups.com <javascript:>
> > <mailto:dendropy-user...@googlegroups.com <javascript:>>.

> > For more options, visit https://groups.google.com/d/optout

> <https://groups.google.com/d/optout>.

>
> --
>
>
>
> --------------------------------------
> Jeet Sukumaran
> --------------------------------------

> jeetsu...@gmail.com <javascript:>

> --------------------------------------
> Blog/Personal Pages:
> http://jeetworks.org/
> GitHub Repositories:

> http://github.com/jeetsukumaran <http://github.com/jeetsukumaran>

> Photographs (as stream):
> http://www.flickr.com/photos/jeetsukumaran/
> <http://www.flickr.com/photos/jeetsukumaran/>
> Photographs (by galleries):
> http://www.flickr.com/photos/jeetsukumaran/sets/

> <http://www.flickr.com/photos/jeetsukumaran/sets/>
> --------------------------------------

>
> --
> You received this message because you are subscribed to the Google
> Groups "DendroPy Users" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to dendropy-user...@googlegroups.com

> <mailto:dendropy-user...@googlegroups.com>.

[Caleb Ji]

That works, thank you for your time!