User: peterlageweg603

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Posts by peterlageweg603

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Installing AntiSMASH for Mac
... I want to install Antismash through conda with the mac terminal. But I got a permission error when performing the command below: conda install -c bioconda antismash Error: ERROR conda.core.link:_execute(568): An error occurred while uninstalling package 'defaults::qt-5.9.7-h468cd18_1'. ...
antismash secondary metabolites written 10 weeks ago by peterlageweg6030
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Comment: C: Extract Tree Topology From Ncbi Taxonomy Database
... Ah thank you for the fast responding and help!! This is exactly what I needed :) ...
written 3 months ago by peterlageweg6030
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Comment: C: Extract Tree Topology From Ncbi Taxonomy Database
... Thanks SMK. I tried this but it does not work. tree.write(features=["sci_name", "rank"], outfile="tree.nw") t_file = Tree("tree.nw") for node in t_file.traverse(): node.name = node.sci_name tree.write(features=["node.name"], outfile="labeled_tree.nw") AttributeErr ...
written 3 months ago by peterlageweg6030
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Comment: C: Extract Tree Topology From Ncbi Taxonomy Database
... Thanks! This works as well. Is there a way to replace the TaxIDs with the scientific names? ...
written 3 months ago by peterlageweg6030
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Comment: C: Extract Tree Topology From Ncbi Taxonomy Database
... Is there a way to replace the TaxIDs with the scientific names? ...
written 3 months ago by peterlageweg6030
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Comment: C: Extract Tree Topology From Ncbi Taxonomy Database
... Thanks for the fast responding! Works like a charm :) ...
written 3 months ago by peterlageweg6030
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Comment: A: Extract Tree Topology From Ncbi Taxonomy Database
... I'm trying this method as well. from ete3 import NCBITaxa ncbi = NCBITaxa() tree = ncbi.get_topology([9606, 9598, 10090, 7707, 8782]) print tree.get_ascii(attributes=["sci_name", "rank"]) Can someone tell me how I can convert the output to a Newick file? ...
written 3 months ago by peterlageweg6030

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