Extract taxonomic lineages from NCBI based on assembly_summary files
This tool is used to create files for use with sourmash tax and
sourmash lca index, for taxonomic summaries. It ingests
assembly summary
files, and produces output file(s) formatted like so:
ident,taxid,superkingdom,phylum,class,order,family,genus,species,strain,taxpath
GCF_900128725.1,9,Bacteria,Pseudomonadota,Gammaproteobacteria,Enterobacterales,Erwiniaceae,Buchnera,Buchnera aphidicola,,2|1224|1236|91347|1903409|32199|9|
GCF_008244535.1,14,Bacteria,Dictyoglomi,Dictyoglomia,Dictyoglomales,Dictyoglomaceae,Dictyoglomus,Dictyoglomus thermophilum,,2|68297|203486|203487|203488|13|14|
GCF_001735525.1,23,Bacteria,Pseudomonadota,Gammaproteobacteria,Alteromonadales,Shewanellaceae,Shewanella,Shewanella colwelliana,,2|1224|1236|135622|267890|22|23|
GCF_019654935.1,23,Bacteria,Pseudomonadota,Gammaproteobacteria,Alteromonadales,Shewanellaceae,Shewanella,Shewanella colwelliana,,2|1224|1236|135622|267890|22|23|
GCF_019655395.1,23,Bacteria,Pseudomonadota,Gammaproteobacteria,Alteromonadales,Shewanellaceae,Shewanella,Shewanella colwelliana,,2|1224|1236|135622|267890|22|23|
If you already have snakemake installed, you can skip this step. If not, you can install with mamba from this directory, with:
mamba env create -f environment.yml
conda activate build-ncbi-lineages
This activates an isolated conda/mamba environment with Snakemake installed. When you're finished running this and want
to return to your base environment, run conda deactivate or close your terminal.
If you don't have
mamba:
- If you have
conda, substitute with conda:conda env create -f environment.yml- If not, you can install mamba (with conda) by following instructions here.
Execute the test:
snakemake -c1
This will generate an output file example.lineages.csv based
on the input file example.assembly_summary.txt. Note that snakemake
will download all of the necessary support files, including NCBI taxonomy files.
The full workflow will build lineages files for the following domains: archaea, fungi, protozoa, bacteria, viral
Run:
snakemake all -c1
This will generate one lineages file per domain, e.g. bacteria.lineages.csv.
The workflow will download the required {domain}.assembly_summary.txt files
(and NCBI taxonomy files, if not download as part of testing, above).
Note, if you want to build a combined lineages file for all domains, use
snakemake combined -c1.
Code based on https://github.com/dib-lab/2018-ncbi-lineages and https://github.com/ctb/2022-assembly-summary-to-lineages.
2023-02-07 NTP, CTB