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Loading UHGG taxonomy fails #32

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Midnighter opened this issue Sep 29, 2020 · 1 comment
Open

Loading UHGG taxonomy fails #32

Midnighter opened this issue Sep 29, 2020 · 1 comment

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@Midnighter
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The EBI has published a Unified Human Gastrointestinal Genome (UHGG) catalogue which includes a taxonomy of their genome clusters. When I try to load it with taxonomy it unfortunately fails. I wonder if the problem lies with taxonomy or EBI providing a bad format.

from taxonomy import Taxonomy

tax = Taxonomy.from_ncbi("taxonomy/nodes.dmp", "taxonomy/names.dmp")
TaxonomyError: Error importing: Not enough fields in nodes.dmp; perhaps names and nodes files are switched?
@Midnighter
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Additionally, taxonomy fails to load the GTDB in Newick format. I have attached different versions
(gtdb.zip) that I can visualize with the ETE toolkit. Sample code:

from taxonomy import Taxonomy


with open("data/taxonomy/ar122_r89.tree") as handle:
    archaea = Taxonomy.from_newick(handle.read())
TaxonomyError: Error importing: Could not parse distance {} as a number

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