Simplified & efficient GISAID interactions.
Project description
gisaid-uploader
Simplified & efficient GISAID interactions.
** This package is in development **
Features to be added soon:
- STARLIMS REST API support for pipelines
- GISAID API download functionality
-
Register for a GISAID account
-
Email GISAID & request a client ID
Installation:
>>> pip install gisaid
Authenticate once:
>>> import gisaid as gs
>>> gs.GiSaid(authenticate=True, client_id="foo",
>>> username="bar", password="foobar", filename="authfile.json")
"Authentication successful"
CSV + fasta file:
>>> import gisaid as gs
>>> x = gs.GiSaid("upload.csv", "fasta.fa")
>>> x.upload()
"93 Successful Uploads"
"15 Failed Uploads"
Collated CSV:
>>> import gisaid as gs
>>> x = gs.GiSaid("collated", "upload.csv")
>>> x.upload()
"93 Successful Uploads"
Upload to a SQL database:
>>> import gisaid as gs
>>> table_name = "foobar"
>>> method = "append"
>>> x = gs.GiSaid("upload.csv", "fasta.fa")
>>> x.upload_sql(table_name, method, conn)
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