gisflu 0.1.10

Access the GISAID Flu database using Python

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