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https://github.com/zyxue/ncbitax2lin
🐞 Convert NCBI taxonomy dump into lineages
https://github.com/zyxue/ncbitax2lin
lineage ncbi ncbi-taxonomy pandas python taxdump taxonomy
Last synced: 14 days ago
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🐞 Convert NCBI taxonomy dump into lineages
- Host: GitHub
- URL: https://github.com/zyxue/ncbitax2lin
- Owner: zyxue
- License: mit
- Created: 2016-04-24T05:41:45.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2022-04-04T15:59:45.000Z (over 2 years ago)
- Last Synced: 2024-08-09T23:44:42.498Z (3 months ago)
- Topics: lineage, ncbi, ncbi-taxonomy, pandas, python, taxdump, taxonomy
- Language: Python
- Homepage:
- Size: 355 KB
- Stars: 135
- Watchers: 8
- Forks: 29
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.txt
Awesome Lists containing this project
README
# NCBItax2lin
[](https://pepy.tech/project/ncbitax2lin)
Convert NCBI taxonomy dump into lineages. An example for [human
(tax_id=9606)](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?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 | | | | |
### Install
ncbitax2lin supports python-3.7, python-3.8, and python-3.9.
```
pip install -U ncbitax2lin
```
### Generate lineages
First download taxonomy dump from NCBI:
```bash
wget -N ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
mkdir -p taxdump && tar zxf taxdump.tar.gz -C ./taxdump
```
Then, run ncbitax2lin
```bash
ncbitax2lin --nodes-file taxdump/nodes.dmp --names-file taxdump/names.dmp
```
By default, the generated lineages will be saved to
`ncbi_lineages_[date_of_utcnow].csv.gz`. The output file can be overwritten with
`--output` option.
## FAQ
**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](https://github.com/zyxue/ncbitax2lin/issues/new).
## Note on `taxdump.tar.gz.md5`
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.
## Used in
* Mahmoudabadi, G., & Phillips, R. (2018). A comprehensive and quantitative exploration of thousands of viral genomes. ELife, 7. https://doi.org/10.7554/eLife.31955
* Dombrowski, N. et al. (2020) Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution, Nature Communications. Springer US, 11(1). doi: 10.1038/s41467-020-17408-w. https://www.nature.com/articles/s41467-020-17408-w
* Schenberger Santos, A. R. et al. (2020) NAD+ biosynthesis in bacteria is controlled by global carbon/ nitrogen levels via PII signaling, Journal of Biological Chemistry, 295(18), pp. 6165–6176. doi: 10.1074/jbc.RA120.012793. https://www.sciencedirect.com/science/article/pii/S0021925817482433
* Villada, J. C., Duran, M. F. and Lee, P. K. H. (2020) Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5' End of ORFeomes, mSystems, 5(4), pp. 1–18. doi: 10.1128/msystems.00613-20. https://msystems.asm.org/content/5/4/e00613-20
* Byadgi, O. et al. (2020) Transcriptome analysis of amyloodinium ocellatum tomonts revealed basic information on the major potential virulence factors, Genes, 11(11), pp. 1–12. doi: 10.3390/genes11111252. https://www.mdpi.com/2073-4425/11/11/1252
## Development
### Install dependencies
```
poetry shell
poetry install
```
### Testing
```
make format
make all
```
### Publish (only for administrator)
```
poetry version [minor/major etc.]
poetry publish --build
```