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Include SFS build

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trvrb committed Apr 17, 2019
1 parent 3afef14 commit e9a3936f5d8f0664037504f697bab527e69fb012
Showing with 35 additions and 0 deletions.
  1. +13 −0 builds/SEATTLE.md
  2. +1 −0 source-data/geo_synonyms.tsv
  3. +21 −0 vdb/seattle_upload.py
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# Seattle Flu Pipeline Notes

## Download

python2 vdb/download.py -db vdb -v seattle --fstem seattle

## Upload

### Fred Hutch sequences

Upload with:

python2 vdb/seattle_upload.py -db vdb -v seattle --source sfs --authors "Seattle Flu Study Consortium" --url https://github.com/seattleflu --title "Seattle Flu Study" --fname seattle.fasta
@@ -2757,6 +2757,7 @@ SanFrancisco USA California SanFrancisco
SanRamon USA California SanRamon
SantaClara USA California SantaClara
SantaFe USA NewMexico SantaFe
Seattle USA Washington Seattle
SilverSpring USA Maryland SilverSpring
SL USA USA USA
Springfield USA Illinois Springfield
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import os, re, time, datetime, csv, sys
import rethinkdb as r
from Bio import SeqIO
from upload import upload
from upload import get_parser

class seattle_upload(upload):
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)

if __name__=="__main__":
parser = get_parser()
args = parser.parse_args()
virus_fasta_fields = {0:'strain', 2:'type', 4:'collection_date', 5:'country', 6:'division', 7:'division'}
sequence_fasta_fields = {0:'strain', 1:'accession', 3:'segment'}
# 0 1 2 3 4 5 6 7
#>FS_10_S1_001|FS_10_S1_001-PB1|H3N2|PB1|XXXX-XX-XX|usa|washington|seattle
setattr(args, 'virus_fasta_fields', virus_fasta_fields)
setattr(args, 'sequence_fasta_fields', sequence_fasta_fields)
connVDB = seattle_upload(**args.__dict__)
connVDB.upload(**args.__dict__)

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