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Currently, we get the genus and species, common name, and kingdom or domain names
```-outfmt "6 qseqid sseqid evalue bitscore staxids sscinames scomnames sskingdoms" \```
Would like to get some …
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Dear MitoZ team,
Thanks for updating and maintaining the repository.
I have a question regarding installing NCBI database inside ete3 package command:
from ete3 import NCBITaxa
ncbi = NCBITaxa(…
ghost updated
5 years ago
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Hi there,
When I run this code (Python 2.7)
`from ete3 import NCBITaxa`
`ncbi = NCBITaxa()`
I get this error
> NCBI database not present yet (first time used?)
> Downloading taxdump.ta…
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Hi, I have tried to make the database using `makeDB.sh -e`. It finished downloading all the necessary files but killed itself when moving onto `mkbwt` step.
These are the files I got from the part…
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Hi, I'm trying to run the LIB command in order to build the DB for Bacteria. I've downloaded the nt.fasta file and ran the command
`python pathoscope2.py LIB -genomeFile ../data/nt.fasta -taxonIds …
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Hi,
May I know is it suitable to do taxonomy prediction for assembled contigs from megahit in kaiju? Thanks in advance.
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- handling taxonomy in local blast - current hack is list of GIs
- identical sequences are sneaking in. How?
- zombie taxa?
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Something has went sour in tidyverse environment
```
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 2
Rules claiming more threads will be scaled down.
Job counts:
…
tpall updated
5 years ago
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test download procedure with a small dataset like ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
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For accurate identification of sequence sources (e.g. when extracting a database for "all cinnamomi") we need to be able to identify all sequences that "belong" to "cinnamomi".
With a simple string…