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Move mumps readme from augur

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trvrb committed Sep 25, 2017
1 parent 29a38b2 commit 2f5453b560b99a8194a17c4e0771eafe1f8f8787
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  2. +1 −0 builds/README.md
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## Download data from VIPR
* paramyxos -> genome search -> data to return = genome -> type "mumps" in search
* select complete genome only (n=104 as of july 2017)
* select all -> download
* download genome fasta with custom format. Fields: GB-SN-SEG-DATE-HOST-COUN-SUBTY-VIRSPEC
* copy vipr fasta file to `fauna/data/mumps_vipr_full.fasta`
## Clean FASTA
```
cd fauna
python vdb/mumps_preprocess_fasta.py --vipr
```
The cleaned fasta is now available at `data/mumps_vipr.fasta`
_Note: this will eventually be incorporated into the Fauna upload script_
## Upload to fauna
`python vdb/mumps_upload.py -db vdb -v mumps --source genbank --locus genome --fname mumps_vipr.fasta`
## Update fauna database
This is needed to populate certain attributes such as author & paper title.
`python vdb/mumps_update.py -db vdb -v mumps --update_citations`
## Download from fauna
`python vdb/mumps_download.py -db vdb -v mumps --fstem mumps --resolve_method choose_genbank`
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* [Ebola virus](EBOLA.md)
* [seasonal influenza virus](FLU.md)
* [avian influenza H7N9 virus](H7N9.md)
* [mumps virus](MUMPS.md)
* [Zika virus](ZIKA.md)

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