antunderwood’s gists

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 / 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 / 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 / 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 / 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 / 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 / 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 / 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 / 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 / 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 <- '[
	{

Anthony Underwood antunderwood