Trouble converting clustal to nexus

Question

[mac03pat]

Used this code:

from Bio import AlignIO

AlignIO.convert('aligned_KS1.clw', 'clustal', 'aligned_KS.nexus', 'nexus')

On this file: https://drive.google.com/open?id=1UX7H1sDdRSVT0I3fXb-rGXbfRZx10hGZ

And received this error:

Traceback (most recent call last):
  File "C:\Users\mac03\AppData\Local\Programs\Python\Python37\MBSProject\KS_tree_builder.py", line 3, in <module>
    tree = Phylo.read('aligned_KS.clw', 'phyloxml')
  File "C:\Users\mac03\AppData\Local\Programs\Python\Python37\lib\site-packages\Bio\Phylo\_io.py", line 63, in read
    tree = next(tree_gen)
  File "C:\Users\mac03\AppData\Local\Programs\Python\Python37\lib\site-packages\Bio\Phylo\_io.py", line 51, in parse
    for tree in getattr(supported_formats[format], 'parse')(fp, **kwargs):
  File "C:\Users\mac03\AppData\Local\Programs\Python\Python37\lib\site-packages\Bio\Phylo\PhyloXMLIO.py", line 98, in parse
    return Parser(file).parse()
  File "C:\Users\mac03\AppData\Local\Programs\Python\Python37\lib\site-packages\Bio\Phylo\PhyloXMLIO.py", line 297, in __init__
    event, root = next(context)
  File "C:\Users\mac03\AppData\Local\Programs\Python\Python37\lib\xml\etree\ElementTree.py", line 1222, in iterator
    yield from pullparser.read_events()
  File "C:\Users\mac03\AppData\Local\Programs\Python\Python37\lib\xml\etree\ElementTree.py", line 1297, in read_events
    raise event
  File "C:\Users\mac03\AppData\Local\Programs\Python\Python37\lib\xml\etree\ElementTree.py", line 1269, in feed
    self._parser.feed(data)
  File "<string>", line None
xml.etree.ElementTree.ParseError: syntax error: line 1, column 0

A new nexus file is created but it's empty.

I am converting to nexus in order to build a phylogenetic tree with this code:

from Bio import Phylo

tree = Phylo.read('aligned_KS.nexus', 'nexus')
tree.ladderize()
Phylo.draw(tree)

Answer 1

[AK]

Hi mac03pat,

Please check out Question: Convert Clustal To Nexus Format In Python. From that discussion the following codes work for me:

from Bio import AlignIO
from Bio import Alphabet

AlignIO.convert('aligned_KS1.clw', 'clustal', 'aligned_KS1.nexus', 'nexus', alphabet=Alphabet.generic_dna)

Results:

$ head aligned_KS1.nexus
#NEXUS
begin data;
    dimensions ntax=19 nchar=1415;
    format datatype=dna missing=? gap=- interleave;
matrix
MG777497.1      ATTGTCATTGTTGGCATGGCTTGCCGACTTCCAGGCGATGTCGATAGCGCCTCGAGCCTATGGAAGTTGT
JX067626.1      ATCGCCGTCGTTGGTATGGCTCTCCAAGTCCCT---GGGGCTAATGATCTGGAAGAATTCTCCCAGCTCT
MG777490.1      ATCGCGATCATTGGTATGGGTTGTAGATTCCCG---GGTGCTGATTCCATTGACGAGTATTGGAATTTGC
MG777492.1      GTTGCCATTATCGGCGCTTCATGTCGCCTACCG---GGCGCCAATAGTATGGAGGAGCTCTGGGACCTCA
MG777500.1      ATAGCCGTTGTCGGTATGGCATGCCGCTTTCCA---GGTGCTAATACAACGGAAGAGTTCTGGGATCTTC