TaxFinder
The TaxFinder module is a library to help with NCBI taxonomy ids.
Install it using pip, preferable into a virtual environment:
$ pip install taxfinder ### TODO: This is not working for now!
### TODO: Use for now:
$ cd path/to/taxfinder
$ pip install -e .
To do this, TaxFinder needs to download and create a databse with taxonomy information. This database needs in the order of 300 MB disc space. To create the database, run
$ taxfinder_update
By default, TaxFinder tries to create the database in the installation directory. If you experience problems or you want to save the database to another path, set the environment variable TFPATH to the desired path. This path must be readable and writable for TaxFinder.
To use TaxFinder, you need to import it and instanciate the main class. This will open the database and also cache your queries so repeated queries are answered faster.
from taxfinder import TaxFinder
TF = TaxFinder()
print(TF.getLineage(9606))
In an interactive session, you can also get help on the TaxFinder methods:
>>> from taxfinder import TaxFinder
>>> help(TaxFinder)
2 maintainers
Release files for taxfinder 0.0.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| taxfinder-0.0.1.tar.gz | 7.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| taxfinder-0.0.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 14.7 kB
Release files / taxfinder-0.0.1.tar.gz
| Download URL | taxfinder-0.0.1.tar.gz |
|---|---|
| Size | 7.1 kB |
| Tags | Source |
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Release files / taxfinder-0.0.1-py3-none-any.whl
| Download URL | taxfinder-0.0.1-py3-none-any.whl |
|---|---|
| Size | 7.6 kB |
| Tags | Python 3 |
|
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No |
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