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Inconsistency in keeping square brackets from node comments from phylogenetic trees (Nexus VS Phylo) #4009

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Gullumluvl opened this issue Jul 29, 2022 · 2 comments
Open

Inconsistency in keeping square brackets from node comments from phylogenetic trees (Nexus VS Phylo) #4009

Gullumluvl opened this issue Jul 29, 2022 · 2 comments
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@etal

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@Gullumluvl
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Hi, I am using Biopython 1.79.

Sorry, I admit this is a detail, but I reference it in case comment parsing is updated in the future. I could participate in that.

Expected behaviour

Comment should have an identical format between Phylo parser and Nexus parser. In particular, without the surrounding square brackets.

Actual behaviour

  1. Using Phylo.read(format="newick"): the square brackets are stripped.
  2. Using Nexus.Nexus() or Phylo.read(format="nexus"): the square brackets are kept.

In details (see below to reproduce):

Bio.Nexus.Nexus parser:            comment a = '[&varX=5]'
Bio.Phylo parser, format="nexus":  comment a = '[&varX=5]'
Bio.Phylo parser, format="newick": comment a = '&NHX:varX=5'
Bio.Phylo parser, format="newick", input line from nexus file: comment a = '&varX=5'

Steps to reproduce

from io import StringIO
from Bio import Phylo
from Bio.Nexus import Nexus


nexus_txt = """Begin trees;
    tree TREE1 = ((a[&varX=5]:1,b[&varX=6,varY=abc]:1):2,c:3):0.5;
End;
"""

NHX_txt = "((a[&NHX:varX=5]:1,b[&NHX:varX=6:varY=abc]:1):2,c:3):0.5;"


nx = Nexus.Nexus(StringIO(nexus_txt))
tree = nx.trees[0]
node_a = tree.node(tree.search_taxon('a'))
print('Bio.Nexus.Nexus parser:            comment a = %r' % node_a.data.comment)

tree = Phylo.read(StringIO(nexus_txt), 'nexus')
node_a = tree.find_any(name='a')
print('Bio.Phylo parser, format="nexus":  comment a = %r' % node_a.comment)

tree = Phylo.read(StringIO(NHX_txt), 'newick')
node_a = tree.find_any(name='a')
print('Bio.Phylo parser, format="newick": comment a = %r' % node_a.comment)

tree = Phylo.read(StringIO(nexus_txt.splitlines()[1].split()[-1]), 'newick')
node_a = tree.find_any(name='a')
print('Bio.Phylo parser, format="newick", input line from nexus file: comment a = %r' % node_a.comment)
@peterjc
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peterjc commented Aug 9, 2022

It was confusing your example didn't use the same Newick tree, e.g.

NHX_txt = "((a[&NHX:varX=5]:1,b[&NHX:varX=6:varY=abc]:1):2,c:3):0.5;"
nexus_txt = f"""Begin trees;
    tree TREE1 = {NHX_txt}
End;
"""

That makes your point much more clearly:

Bio.Nexus.Nexus parser:            comment a = '[&NHX:varX=5]'
Bio.Phylo parser, format="nexus":  comment a = '[&NHX:varX=5]'
Bio.Phylo parser, format="newick": comment a = '&NHX:varX=5'
Bio.Phylo parser, format="newick", input line from nexus file: comment a = '&NHX:varX=5'

@Gullumluvl
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Yes, this would show the parsing behavior more clearly.

The difference was there because comment formatting in NHX differs from comment formatting in Nexus trees. From what I've seen.

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@etal @peterjc @Gullumluvl