MattOates’s gists

MattOates / named_tuple_dumping_fail.py

Created May 13, 2019 16:55

	from typing import NamedTuple
	import json


	class NamedTupleJSONEncoder(json.JSONEncoder):

	def encode(self, o):
	print(f"Encoding {type(o)}")
	return super().encode(o)

MattOates / sketch_of_concept_trigger.sql

Created January 14, 2019 15:36

	CREATE TABLE patient (
	name text,
	administrative_gender uuid references concept.concept_cid,
	ethnicity uuid references concept.concept_cid,
	phenotypic_sex_cid uuid references concept.concept_cid,

	);

	-- Parametric trigger for validating concept FK against sets of codesystems
	-- concept_ind_codesystem(concept_field_name, array_of_codesystems)

MattOates / day2_task2.pl6

Last active December 2, 2018 16:43

https://adventofcode.com/2018/day/2

	#!/usr/bin/env perl6

	sub character_differences(Str $str1, Str $str2) {
	$str1.comb Z~~ $str2.comb
	}

	sub hamming_distance(Str $str1, Str $str2) {
	my @differences = character_differences($str1, $str2);
	return @differences.grep(* == False).elems;
	}

MattOates / index.html

Created November 14, 2018 22:11

Time: <span id="clockDisplay"></span>

MattOates / main.p6

Created October 16, 2018 15:04

6pad gist test

	say "Ohai!";

	for ^10 -> $stuff {
	say $stuff if $stuff.is-prime;
	}

MattOates / hackerrank_bench.p6

Last active September 13, 2018 09:07

Some additional benched P6 examples from Tyil's Hackerrank post https://www.tyil.nl/post/2018/09/13/hackerrank-solutions-python3-and-perl6-part-1/

	use Stats;

	sub bench($name, &code) {

	my ($start,$end);
	my @times;

	for 1..100 {
	$start = now;
	code();

MattOates / mandelbrot.p6

Last active August 13, 2018 19:02

Quick and dirty script for plotting the Mandelbrot set in the terminal using unicode shading characters. An example invocation: perl6 mandelbrot.p6 --mid-x=-0.73e0 --mid-y=0.246e0 --zoom=0.03e0 --height=300

	use Terminal::Width;

	sub is-mandelbrot(Complex $z0, int $max=100) {
	my Complex $z = $z0;
	for ^$max -> $n {
	return $n if ($z.abs() > 2e0);
	$z = $z**2 + $z0;
	}
	return $max;
	}

MattOates / build_chromosome_files.p6

Created August 3, 2018 15:42

So running the below with the pathological case ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/BUILD.37.3/CHR_01/hs_ref_GRCh37.p5_chr1.fa.gz

	#!/usr/bin/env perl6
	use Compress::Zlib;
	use IO::String;

	my $DATA_DIR = %*ENV<DATA_DIR> // '/Users/matt/data/reference/GRCh37/sequence/dna';

	for dir($DATA_DIR).grep(/chr\d+\.fa\.gz/) -> $file {
	my $out_file = $file.IO.extension('txt', :2parts).open(:w);
	my $chromosome = IO::String.new(buffer=>gzslurp($file));
	for $chromosome.lines -> $line {

MattOates / build_chromosome_files.p6

Created August 3, 2018 15:42

So running the below with the pathological case ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/BUILD.37.3/CHR_01/hs_ref_GRCh37.p5_chr1.fa.gz

	#!/usr/bin/env perl6
	use Compress::Zlib;
	use IO::String;

	my $DATA_DIR = %*ENV<DATA_DIR> // '/Users/matt/data/reference/GRCh37/sequence/dna';

	for dir($DATA_DIR).grep(/chr\d+\.fa\.gz/) -> $file {
	my $out_file = $file.IO.extension('txt', :2parts).open(:w);
	my $chromosome = IO::String.new(buffer=>gzslurp($file));
	for $chromosome.lines -> $line {

MattOates / build_chromosome_files.p6

Created August 3, 2018 15:42

So running the below with the pathological case ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/BUILD.37.3/CHR_01/hs_ref_GRCh37.p5_chr1.fa.gz

	#!/usr/bin/env perl6
	use Compress::Zlib;
	use IO::String;

	my $DATA_DIR = %*ENV<DATA_DIR> // '/Users/matt/data/reference/GRCh37/sequence/dna';

	for dir($DATA_DIR).grep(/chr\d+\.fa\.gz/) -> $file {
	my $out_file = $file.IO.extension('txt', :2parts).open(:w);
	my $chromosome = IO::String.new(buffer=>gzslurp($file));
	for $chromosome.lines -> $line {

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