gisaid 1.0.5b0

Simplified & efficient GISAID interactions.

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

---

1. Register for a GISAID account

2. 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)