Package: ncbitax2lin
NCBItax2linConvert NCBI taxonomy dump into lineages. An example forhuman
(tax_id=9606)is liketax_idsuperkingdomphylumclassorderfamilygenusspeciesfamily1formagenus1infraclassinfraorderkingdomno rankno rank1no rank10no rank11no rank12no rank13no rank14no rank15no rank16no rank17no rank18no rank19no rank2no rank20no rank21no rank22no rank3no rank4no rank5no rank6no rank7no rank8no rank9parvorderspecies groupspecies subgroupspecies1subclasssubfamilysubgenussubkingdomsubordersubphylumsubspeciessubtribesuperclasssuperfamilysuperordersuperorder1superphylumtribevarietas9606EukaryotaChordataMammaliaPrimatesHominidaeHomoHomo sapiensSimiiformesMetazoacellular organismsOpisthokontaDipnotetrapodomorphaTetrapodaAmniotaTheriaEutheriaBoreoeutheriaEumetazoaBilateriaDeuterostomiaVertebrataGnathostomataTeleostomiEuteleostomiSarcopterygiiCatarrhiniHomininaeHaplorrhiniCraniataHominoideaEuarchontogliresInstallncbitax2lin supports python-3.7, python-3.8, and python-3.9.pip install -U ncbitax2linGenerate lineagesFirst download taxonomy dump from NCBI:wget-Nftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
mkdir-ptaxdump&&tarzxftaxdump.tar.gz-C./taxdumpThen, run ncbitax2linncbitax2lin--nodes-filetaxdump/nodes.dmp--names-filetaxdump/names.dmpBy default, the generated lineages will be saved toncbi_lineages_[date_of_utcnow].csv.gz. The output file can be overwritten with--outputoption.FAQQ: 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 onnucl_*accession2taxid.gzfiles fromftp://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 newissue.Note ontaxdump.tar.gz.md5It appears that NCBI periodically regeneratestaxdump.tar.gzandtaxdump.tar.gz.md5even when its content is still the same. I am not sure how
their regeneration works, buttaxdump.tar.gz.md5will differ simply because
of a different timestamp.Used inMahmoudabadi, G., & Phillips, R. (2018). A comprehensive and quantitative exploration of thousands of viral genomes. ELife, 7.https://doi.org/10.7554/eLife.31955Dombrowski, 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-wSchenberger 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/S0021925817482433Villada, 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/e00613-20Byadgi, 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/2073-4425/11/11/1252DevelopmentInstall dependenciespoetry shell
poetry installTestingmake format
make allPublish (only for administrator)poetry version [minor/major etc.]
poetry publish --build