Question: convert GCF code to outer leaf Organism name
0
gravatar for peterlageweg603
7 months ago by
peterlageweg60310 wrote:

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.

ADD COMMENTlink written 7 months ago by peterlageweg60310
1
gravatar for genomax
7 months ago by
genomax84k
United States
genomax84k wrote:

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)
ADD COMMENTlink modified 7 months ago • written 7 months ago by genomax84k

I'm sorry! GCF_001598035

ADD REPLYlink written 7 months ago by peterlageweg60310
1

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.

ADD REPLYlink written 7 months ago by genomax84k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 815 users visited in the last hour