Create next-strain csv file

TYMichaelsen / covid19

Bioinformatic pipelines used to assemble SARS-CoV-2 genomes from DK

GNU General Public License v3.0

3 stars 3 forks source link

Create next-strain csv file #42

Closed tomersagi closed 4 years ago

tomersagi commented 4 years ago

[x] Update mysql conversion script to latest tsv file
[x] Add municipality code to mysql convert script
[x] Create MySQL query to extract data and group by week, municipality and strain
[x] Find a data source with Long. Lat. for each Danish municipality @Miro
[x] Add fake ID for each group
[x] Create a script to extract result, filter out less than 3 rows and write to csv

tomersagi commented 4 years ago

Query output: ID sample_date - start of a week epi_week - elapsed from beginning of the epidemic country - fixed = DK01 adm1 - Region
submission_org_code - Municipality lineage - GlobalClade assignment lineage_support (SC?) - Not available uk_lineage - Thomas? - column: highres_clade primary_uk_lineage - Thomas? - column: nextstrain_clade

longitude and latitude according to micro react format https://microreact.org/instructions

tomersagi commented 4 years ago

[x] Figure out how to color the nodes
[x] Figure out how to add a side window with the graph like in the UK example

tomersagi commented 4 years ago

[x] tree_raw.nwk is in the DenmarkOnly folder - see if we can integrate it into micro-react
[x] Ask Mads if he wants a phylogenetic tree view as well (UK example doesn't have it)