JD Bothma jbothma

The relationship between isolates, sequences, and FASTA headers depends on the assembly level of the genome:

Complete Genomes

For a single complete bacterial genome (one isolate):

The FASTA file contains multiple sequences (one per chromosome/plasmid)
Each header represents a different replicon (chromosome, plasmid, or organelle)

Example from one Klebsiella isolate:

This task will give you practice

making sense of an unfamiliar API using its documentation
handling, transforming and combining data, and coming up with data structures that enable you to present it easily
dealing with interdependent API responses that complete in an arbitrary order, and ideally presenting progressively more information to the user as more data becomes available

Focus on logic and clean understandable code rather than visual design.


	# Source: song/templates/deployment.yaml
	apiVersion: apps/v1
	kind: Deployment
	metadata:
	name: song
	labels:
	app.kubernetes.io/name: song
	app.kubernetes.io/instance: song
	spec:

	# python scrape_wikipedia.py countries.json intros flags
	#
	# countries.json is countries search facet.

	import requests
	from lxml import html
	import json
	from sys import argv
	import re
	from normality.cleaning import collapse_spaces

	{
	"ocid": "ocds-0E7232F7-67EC-42BD-B081-3370171F20B7",
	"id": "ocds-0E7232F7-67EC-42BD-B081-3370171F20B7-2022-03-30 13:40:05.8245389",
	"date": "2022-03-30T13:40:05",
	"initiationType": "tender",
	"tender": {
	"id": "3622",
	"title": "LMN 03/2021",
	"status": "active",
	"mainProcurementCategory": "Administrative and support activities",

	{
	"countries": {
	"af": {
	"positions": {
	"us-cia-b1efcaa124e747b3612a9e4191f58ecef8d4f0e2": {
	"position_name": "Deputy Prime Minister",
	"counts": {
	"total": 3,
	"current": 3,
	"ended": 0,

	{
	"$schema": "https://vega.github.io/schema/vega/v5.json",
	"description": "A basic grouped bar chart example.",
	"width": 300,
	"height": 240,
	"padding": 5,
	"data": [
	{
	"name": "table",
	"values": [

	Every country probably has its own chart of accounts.

	Most of the south african chart doesn't fit in the open fiscal data package standard.

	Sometimes you want to impose an ordering on items in a summary. Often the account numbering isn't the correct ordering for long. On muni money we captured that ordering alongside the codes and dimensions.