-
`ngd --taxids` seems to require `gimme_taxa.py` have the `-j`. Not sure if you want to update the documentation or one of the scripts?
```
$ gimme_taxa.py -o taxids.txt Hyphomicrobiales
$ ngd --d…
-
For new frontend, rework wikidata queries to get metadata + list of available wikipedia pages in different languages starting from ncbi taxid.
For the moment the reference query is:
```sparql
S…
-
## Bug report
### Expected behavior and actual behavior
Changes to objects passed as input should trigger new runs when using `-resume`. When changing an object's structure, e.g. putting it in …
-
error message should say invalid protein accession instead of
no canonical for 08697-2, mapping not done
-
From saurin_jani@yahoo.com
>Is there any SOAP/Webservices running which allow
>users to query database to retrive dataset on
>perticular species or ontology process?
This could be part of …
-
### Description of feature
Currently only strain level is allowed/feasible to be used within taxid input.
Solving higher tax levels like species will come with problems:
More than one strain wi…
-
Hi, I encontered with a new error in running hecatomb v1.3.2, here is the related log information:
```
15:23:41.923 [WARN] taxid 1965493 was merged into 3070820
15:23:41.923 [WARN] taxid 45219 wa…
-
Hi,
I'm wondering where `gtdb_ver95_alllca_taxid.csv.tar.gz` is coming from? Have you written it by yourself or downloaded it somewhere? I'm using your pipeline to analyze the microbiome of Austral…
-
The `centrifuge-inspect` script uses the `imp` module which has been removed in python 3.12 (https://docs.python.org/dev/whatsnew/3.12.html#imp).
This also causes `centrifuge-kreport` to produce wr…
-
Downloading HMMER database of tax ID taxid as "4751" to /home/xly/mambaforge/envs/fun/lib/python3.8/site-packages/data/hmmer/4751
Note that this can take a long time for large taxonomic levels
cd /h…