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Anthony Underwood antunderwood

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@antunderwood
antunderwood / weather.csv
Created March 15, 2022 18:01
Seattle Weather
We can't make this file beautiful and searchable because it's too large.
"DATE","PRCP","TMAX","TMIN","RAIN"
"1948-01-01",0.47,51,42,"TRUE"
"1948-01-02",0.59,45,36,"TRUE"
"1948-01-03",0.42,45,35,"TRUE"
"1948-01-04",0.31,45,34,"TRUE"
"1948-01-05",0.17,45,32,"TRUE"
"1948-01-06",0.44,48,39,"TRUE"
"1948-01-07",0.41,50,40,"TRUE"
"1948-01-08",0.04,48,35,"TRUE"
"1948-01-09",0.12,50,31,"TRUE"
@antunderwood
antunderwood / dist_matrix.csv
Created November 6, 2021 12:46
0 1 8 9
1 0 7 8
8 7 0 1
9 8 1 0
@antunderwood
antunderwood / tree.nwk
Created June 14, 2021 11:24
COG-UK SARS-CoV-2 tree 2021-06-14
This file has been truncated, but you can view the full file.
(Wuhan/WH04/2020:0,((France/HDF-100002823145/2021:0,(France/HDF-100002521356/2021:0.000300973,(Germany/NW-RKI-I-088561/2021:0.000401298,Germany/NW-RKI-I-153620/2021:0.000167207,Germany/NW-RKI-I-088632/2021:0.000100324,Germany/NW-RKI-I-088607/2021:6.68829e-05,Germany/NW-RKI-I-069106/2021:0.00023409,(Germany/NW-RKI-I-153674/2021:0,(Germany/NW-RKI-I-088572/2021:6.68829e-05,Germany/NW-RKI-I-088616/2021:0.000133766,(Germany/NW-RKI-I-145025/2021:6.68829e-05,Germany/NW-RKI-I-144938/2021:0.000167207):6.68829e-05,Germany/NW-RKI-I-069031/2021:0.000100324,Germany/NW-RKI-I-145007/2021:0.000133766,Germany/NW-RKI-I-069084/2021:3.34415e-05,Germany/NW-RKI-I-144929/2021:6.68829e-05):3.34415e-05,(Germany/NW-RKI-I-088575/2021:0.000100324,Germany/NW-RKI-I-088568/2021:0.000100324):3.34415e-05,Germany/NW-RKI-I-088586/2021:0.000133766):3.34415e-05):0.000635387):6.6883e-05):6.68829e-05,((Denmark/DCGC-94791/2021:6.68829e-05,Denmark/DCGC-72175/2021:6.68829e-05):3.34415e-05,USA/IL-CDC-ASC210061804/2021:0.000133766):3.34415e-05,(India/T
@antunderwood
antunderwood / colours.csv
Last active June 21, 2021 17:12
id colour
1127 #696969
8081 #fd125b
2/C/53/NMD7 #0fc060
209-36/84 #a65651
E701 #c0135c
E736 #a65651
ERL022789 #ab2e94
ERL023784 #696969
ERL032126 #efe900
@antunderwood
antunderwood / graph.json
Created May 31, 2021 22:24
This file has been truncated, but you can view the full file.
{
"directed": true,
"graph": {},
"links": [
{
"coverage": 1.0,
"identity": 0.997,
"source": "card:ARO:3000005",
"target": "ncbi:WP_063856692.1",
"type": "RBH"
@antunderwood
antunderwood / variants_wide.csv
Created December 2, 2020 14:06
Sample D614G N439K P323I A222V Y453F
1 D N P A F
2 D N P A F
3 D K I A Y
4 G N I V Y
5 G K P V F
@antunderwood
antunderwood / silvia_mock_data.csv
Created December 2, 2020 10:51
Sample position nt
Reference 8782 T
Reference 13066 T
Reference 17858 A
Reference 18060 C
Reference 23403 A
ARG_1 8782 C
ARG_1 13066 T
ARG_1 17858 G
ARG_1 18060 C
@antunderwood
antunderwood / variants.csv
Last active December 2, 2020 09:44
Sample variant allele
1 D614G D
1 N439K N
1 P323I P
1 A222V A
1 Y453F F
2 D614G D
2 N439K N
2 P323I P
2 A222V A
@antunderwood
antunderwood / MICs.tsv
Created October 3, 2020 10:36
Concordance dataset
We can't make this file beautiful and searchable because it's too large.
ROW_IDX COUNTRY_A LABORATORY ORIGIN PATIENT_ID LAST_NAME FIRST_NAME SEX DATE_BIRTH AGE PAT_TYPE WARD INSTITUT DEPARTMENT WARD_TYPE DATE_ADMIS SPEC_NUM SPEC_DATE SPEC_TYPE LOCAL_SPEC SPEC_CODE SPEC_REAS ISOL_NUM ORGANISM LOCAL_ORG ORG_TYPE SEROTYPE MRSA VRE BETA_LACT ESBL CARBAPENEM MRSA_SCRN INDUC_CLI COMMENT DATE_DATA AMC_NM AMK_NM AMP_NM ATM_NM AZM_NM CAZ_NM CEP_NM CFM_NM CHL_NM CIP_NM CLI_NM COL_NM COP_NM CRO_NM CSL_NM CTX_NM CXA_NM CXM_NM CZO_NM DAP_NM DOR_NM ENR_NM ERY_NM ETP_NM FEP_NM FOX_NM GEN_NM IPM_NM LNZ_NM LVX_NM MAN_NM MEM_NM MFX_NM MNO_NM NAL_NM NOR_NM NTZ_NM OFX_NM OXA_NM PEN_NM PIP_NM QDA_NM RIF_NM SAM_NM SPT_NM STR_NM SXT_NM TCC_NM TCY_NM TEC_NM TGC_NM TOB_NM TZP_NM VAN_NM
0.00000 COL RET G18000002 RB 141 eco eco - 2020-09-30 16 16 >2 <=0.5 >32 <=0.12 <=0.5 8 16 >8 <=0.25 <=0.25 >16 <=0.5 8
1.00000 COL RET G18000009 RB 149 kpn kpn - 2020-09-30 >32 2 >2 <=0.5 >32 >4 <=0.5 <=1 <=4 >8 8
@antunderwood
antunderwood / ast_genes.Rmd
Created September 12, 2020 09:07
Code to plot stacked charts for AST and AMR loci
---
title: "Plotting stacked AST/AMR data"
output: html_notebook
---
Read in some data. I've used JSON so I can have the data in this text file
```{r message=FALSE, warning=FALSE}
library(jsonlite)
ast_gene_json <- '[
{