Convert NCBI taxonomy dump into lineages. An example for human (tax_id=9606) is like
| tax_id | superkingdom | phylum | class | order | family | genus | species | family1 | forma | genus1 | infraclass | infraorder | kingdom | no rank | no rank1 | no rank10 | no rank11 | no rank12 | no rank13 | no rank14 | no rank15 | no rank16 | no rank17 | no rank18 | no rank19 | no rank2 | no rank20 | no rank21 | no rank22 | no rank3 | no rank4 | no rank5 | no rank6 | no rank7 | no rank8 | no rank9 | parvorder | species group | species subgroup | species1 | subclass | subfamily | subgenus | subkingdom | suborder | subphylum | subspecies | subtribe | superclass | superfamily | superorder | superorder1 | superphylum | tribe | varietas |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9606 | Eukaryota | Chordata | Mammalia | Primates | Hominidae | Homo | Homo sapiens | Simiiformes | Metazoa | cellular organisms | Opisthokonta | Dipnotetrapodomorpha | Tetrapoda | Amniota | Theria | Eutheria | Boreoeutheria | Eumetazoa | Bilateria | Deuterostomia | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Catarrhini | Homininae | Haplorrhini | Craniata | Hominoidea | Euarchontoglires |
ncbitax2lin supports python-3.7, python-3.8, and python-3.9.
pip install -U ncbitax2lin
First download taxonomy dump from NCBI:
wget -N ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
mkdir -p taxdump && tar zxf taxdump.tar.gz -C ./taxdumpThen, run ncbitax2lin
ncbitax2lin --nodes-file taxdump/nodes.dmp --names-file taxdump/names.dmpBy default, the generated lineages will be saved to
ncbi_lineages_[date_of_utcnow].csv.gz. The output file can be overwritten with
--output option.
Q: I have a large number of sequences with their corresponding accession numbers from NCBI, how to get their lineages?
A: First, you need to map accession numbers (GI is deprecated) to tax IDs
based on nucl_*accession2taxid.gz files from
ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/. Secondly, you can trace a
sequence's whole lineage based on its tax ID. The tax-id-to-lineage mapping is
what NCBItax2lin can generate for you.
If you have any question about this project, please feel free to create a new issue.
It appears that NCBI periodically regenerates taxdump.tar.gz and
taxdump.tar.gz.md5 even when its content is still the same. I am not sure how
their regeneration works, but taxdump.tar.gz.md5 will differ simply because
of a different timestamp.
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poetry shell
poetry install
make format
make all
poetry version [minor/major etc.]
poetry publish --build