convert GCF code to outer leaf Organism name
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2.1 years ago

Hi all!

I have a phylogenetic tree with GCF numbers as outer leaves. I would like to convert these numbers into species names. I already tried to solve this with ete3 within Python or Archaeopteryx to download this information from NCBI. This did not work out. Would be great if someone knows the solution.

Tree-format is newick.

phylogeny archaeopteryx figtree ete3 • 492 views
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2.1 years ago
GenoMax 110k

Are these GCF NCBI assembly accession numbers? If so, using EntrezDirect:

$ esearch -db assembly -query "GCF_000008865" | efetch -format docsum | xtract -pattern DocumentSummary -element AssemblyAccession,Organism
GCF_000008865.2 Escherichia coli O157:H7 str. Sakai (E. coli)
GCF_000008865.1 Escherichia coli O157:H7 str. Sakai (E. coli)
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I'm sorry! GCF_001598035

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Here you go:

$ esearch -db assembly -query "GCF_001598035" | efetch -format docsum | xtract -pattern DocumentSummary -element AssemblyAccession,Organism
GCF_001598035.1 Streptococcus halotolerans (firmicutes)

Remove AssemblyAccession from command above if you just want the name.

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