fludb - Uploading Vaccine Sequences and Metadata

[elginakin]

Fludb should be modified to handle multiple input FASTA and metadata files that have identical column names. For now, I am only using upload_gisaid.py to handle this upload after uploading any circulating strain sequences. This works pretty well since all vaccine strain sequences and metadata can be cleanly stored in a gisaid collection and subsequently downloaded. However, it would be useful to write an upload script which would handle concatenation of sequence and metadata automatically instead of manual concatenation or multiple upload instances.

Similar to issue #190

[elginakin]

Solution: eaabe1e

I rewrote upload_vaccine.py to ingest only a GISAID FASTA with the following header schema:

• Isolate name | Isolate ID | Collection date | Passage details/history | Segment number | Type | Lineage

Type and Name were necessary since we don't pass any of the vaccine sequences through flusort.py before uploading to fludb.

No metadata is needed.