bede’s gists

bede / ukge2024-green-beating-cons.tsv

Last active July 5, 2024 18:14

UK General Election 2024-07-04: constituencies in which Greens beat Conservatives

	constituency	GRN	CON	delta	winner
0	Brighton Pavilion	28809	3975	24834	GRN
1	Bristol Central	24539	1998	22541	GRN
2	Hackney South and Shoreditch	9987	2076	7911	LAB
3	Bristol East	14142	6435	7707	LAB
4	Lewisham North	9685	2701	6984	LAB
5	Walthamstow	9176	2353	6823	LAB
6	Sheffield Central	8283	2339	5944	LAB
7	Bristol South	10855	4947	5908	LAB
8	North Herefordshire	21736	15842	5894	GRN

bede / bioinformatics.patch

Created January 10, 2024 14:08

Necessary modifications to oup-authoring-template.tex for Oxford Bioinformatics submission

	22,23c22,23
	< \documentclass[unnumsec,webpdf,contemporary,large]{oup-authoring-template}%
	< %\documentclass[unnumsec,webpdf,contemporary,large,namedate]{oup-authoring-template}% uncomment this line for author year citations and comment the above
	---
	> % \documentclass[unnumsec,webpdf,contemporary,large]{oup-authoring-template}%
	> \documentclass[unnumsec,webpdf,contemporary,large,namedate]{oup-authoring-template}% uncomment this line for author year citations and comment the above
	957,958c957,958
	< %\bibliographystyle{abbrvnat}
	< %\bibliography{reference}
	---

bede / concat_by_barcode.py

Last active August 8, 2024 10:51

Concatenate demultiplexed ONT FASTQs by barcode (for one or more runs)

	"""
	Purpose: Concatenate demultiplexed FASTQs by barcode for one or more ONT runs
	Usage: python concat_by_barcode.py run1/fastq_pass run2/fastq_pass -o output/
	Author: Bede Constantinides
	"""

	import subprocess
	import sys
	import argparse
	from collections import defaultdict

bede / custom_check.py

Last active May 26, 2023 15:49

Pandera MWE – I want a single failure case when region_is_valid fails indicating the sample_name of the row that failed (cDNA-VOC-1-v4-1)

	from io import StringIO

	import pandas as pd
	import pandera as pa
	import pandera.extensions as extensions
	from pandera.typing import Index, Series

	csv_string = """
	sample_name,country,region
	cDNA-VOC-1-v4-1,USA,Bretagne

bede / split_summary_by_barcode.py

Created February 11, 2021 10:25

Split Guppy sequencing summaries by barcode

	def split_summary_by_barcode(summary_path, out_dir, run_name):
	'''Given a sequencing summary file path, write per barcode summaries to an output directory'''

	dtypes = {
	'filename_fastq': 'object',
	'filename_fast5': 'object',
	'read_id': 'object',
	'run_id': 'category',
	'channel': 'int64',
	'mux': 'int64',

bede / widget.py

Created January 28, 2021 09:15

	import pandas as pd
	from bokeh.models.widgets import Select
	from bokeh.layouts import widgetbox
	from bokeh.models import ColumnDataSource, DataTable, TableColumn, CustomJS
	from bokeh.io import show, output_file, output_notebook, reset_output
	from bokeh.layouts import row, column, layout


	raw_data = {'ORG': ['APPLE', 'ORANGE', 'MELON'],
	'APPROVED': [5, 10, 15],

bede / cluster_df.py

Last active May 8, 2019 12:53

Distance matrix clustering

	import pandas as pd
	from scipy.spatial.distance import squareform
	from scipy.cluster.hierarchy import fcluster, linkage

	def cluster_df(df, method='single', threshold=100):
	'''
	Accepts a square distance matrix as an indexed DataFrame and returns a dict of index keyed flat clusters
	Performs single linkage clustering by default, see scipy.cluster.hierarchy.linkage docs for others
	'''

bede / Dockerfile

Created July 27, 2017 21:27

IVA Ubuntu Dockerfile

	FROM ubuntu:16.04

	RUN apt-get update && \
	apt-get --yes install \
	kmc smalt python3-pip zlib1g-dev libncurses5-dev libncursesw5-dev mummer samtools

	RUN pip3 install iva

	ENTRYPOINT ["iva"]

bede / simple_python3_parallelism.ipynb

Last active January 23, 2017 13:17

Simple Python3 parallelism

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bede / lists_generators_and_laziness.ipynb

Last active August 17, 2016 13:11

Generators vs. lists for sequence filtering

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Bede Constantinides bede