gisflu
Access the GISAID Flu database using Python. Inspired by GISAIDR, which is an R package for accessing the EpiCoV, EpiRSV and EpiPox database of GISAID.
install
# use pip
pip install gisflu
# use pdm
pdm add gisflu
login
import gisflu
# login with provided username and password
cred = gisflu.login("myusername", "mypassword")
# login using environment variables
cred = gisflu.login()
If use environment variables to login, you should export GISFLU_USERNAME and GISFLU_PASSWORD in your environment, or save them as a .env file in the current working directory.
search
cred = gisflu.login()
gisflu.search(cred, type=["A"], HA=["3"], NA=["2"],
collectDateFrom="2020-01-01", recordLimit=10)
download
cred = gisflu.login()
isolateIds = ["EPI_ISL_19185107", "EPI_ISL_19151100"]
gisflu.download(cred, isolateIds, downloadType="protein", segments=["HA", "NA"],
filename="records.fasta")
verbose output
gisflu.log()
This function will activate detailed console logging
1 maintainer
Metadata
1 maintainer
Release files for gisflu 0.1.10
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| gisflu-0.1.10.tar.gz | 9.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| gisflu-0.1.10-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 21.6 kB
Release files / gisflu-0.1.10.tar.gz
| Download URL | gisflu-0.1.10.tar.gz |
|---|---|
| Size | 9.8 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
pdm/2.22.3 CPython/3.10.12 Linux/5.15.167.4-microsoft-standard-WSL2
|
Release files / gisflu-0.1.10-py3-none-any.whl
| Download URL | gisflu-0.1.10-py3-none-any.whl |
|---|---|
| Size | 11.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
455a60dbc60250747fb504e4bb4c9df7e95c54b61a7dffe7b5e5251d32dc846a
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
pdm/2.22.3 CPython/3.10.12 Linux/5.15.167.4-microsoft-standard-WSL2
|
