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I have created mmseq database with ncbi nt, and added taxonomy information. To shorter the search time, I am trying to create a small database with a certain number of species. I have got the ncbi ta…
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Should be a double query:
- one on the taxid
- one on the sciname if the species has no taxid in wikidata
See what identifiers to get back.
See also #6
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if 10239 in ncbi.get_lineage(int(sp)):
File "/home/jingtian/software/miniconda3/envs/py3/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 241, in get_lineage
raise ValueE…
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Dear Dr. Lind,
I'm generating a custom eukdetect db and I'm stucked at get_uncomputed_taxid_per_busco.py. It fails with the following message:
"""
python /home/qi47rin/proj/00-git/EukD…
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Hi everyone
I'm writing this here in hope that someone will solve this issue as this is already an unsolved issue as per the thread, https://github.com/DerrickWood/kraken2/issues/291
So, I fac…
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**Describe the bug**
The rabies genome package includes invalid host taxon ids that cannot be fetched as a taxonomy package.
**To Reproduce**
1. Download rabies virus genome package with `da…
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> Given a list of binomial names, how can I get accession ids and sequences?
```
For each database in ['plant', 'vertebrate', 'invertebrate] do
taxids = restez::list_db_ids() |>
restez::gb…
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Hi all,
Thanks so much for your wonderful works.
I have download s pre-built kraken2 database (PlusPFP) from https://benlangmead.github.io/aws-indexes/k2. However, some taxids in this database d…
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Although I can download most files in advance, it appears that some downloads are hardcoded into the source?
Specifically:
```
./ui/egapx.py: taxids_file = urlopen("
[https://ftp.ncbi.nlm.nih.g…
OH-AU updated
18 hours ago
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Metapro is missing the taxid_trees file, or whatever file is supposed to be found in that folder. The lib_downloader.py script seems to have completed successfully, but no file or folder with that nam…