zachcp’s gists

zachcp / Makefile

Last active January 2, 2023 23:50

Experiment with Cyber for Fasta

	run:
	./cyber readfq.cy < test.fasta

	# 190 Mb
	downloadref:
	wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/metagenomes/human_skin_metagenome/latest_assembly_versions/GCA_013297495.1_ASM1329749v1/GCA_013297495.1_ASM1329749v1_genomic.fna.gz
	gunzip GCA_013297495.1_ASM1329749v1_genomic.fna.gz


	test_cy:

zachcp / index.html

Created November 27, 2022 19:07

Example of uploading and parsing a GBK file with Pyodide + Biopython

	<!DOCTYPE html>
	<html>
	<head>
	<script src="https://cdn.jsdelivr.net/pyodide/v0.21.3/full/pyodide.js"></script>
	</head>
	<body>
	Pyodide test page <br>
	Open your browser console to see Pyodide output

	<p>You can execute any Python code. Just enter something in the box below and click the button.</p>

zachcp / molt-to-svg.R

Created October 5, 2022 18:44

Molecule in GGPlot Via SVG

	library(dplyr)
	library(depict)
	library(grid)
	library(ggplot2)
	library(svgparser)

	# SVG code to make background box transparent
	my_css = '
	rect {
	fill: none;

zachcp / benchmarks.R

Created September 19, 2022 14:22

Metabolomics benchmarks update

	# install.packages("microbenchmark")
	# install.packages("plyr")
	#
	# install.packages("rcdk")
	# install.packages("OrgMassSpecR")
	# install.packages("CHNOSZ")
	#
	# BiocManager::install("Rdisop")
	# BiocManager::install("MetaboCoreUtils")
	#

zachcp / List FK Relationships

Last active March 3, 2021 16:32

Foreign Key Ordering

	select kcu.table_schema \|\| '.' \|\|kcu.table_name as foreign_table,
	'>-' as rel,
	rel_tco.table_schema \|\| '.' \|\| rel_tco.table_name as primary_table,
	string_agg(kcu.column_name, ', ') as fk_columns,
	kcu.constraint_name
	from information_schema.table_constraints tco
	join information_schema.key_column_usage kcu
	on tco.constraint_schema = kcu.constraint_schema
	and tco.constraint_name = kcu.constraint_name
	join information_schema.referential_constraints rco

zachcp / download.sh

Last active August 13, 2020 21:59

NPAtlas DataLevin Test

	wget https://www.npatlas.org/custom/versions/np_atlas_2020_06/NPAtlas_download.json

zachcp / Import Poacket.scpt

Created February 14, 2020 12:39

Pocket-to-DevonThink

	-- POCKET2DEVONTHINK
	-- script imports articles from a local Pocket for Mac app into the inbox of the current Devonthink database
	-- script comes with the use-it-like-you-want-to-and-dont-blame-me licence
	-- last changed on Jan 5, 2015
	-- recent changes: errorhandling; pdfs for pocket records without mime setting; conditional searches

	-- USER SETTINGS; please adopt to your needs
	--loop_min/max define the range of pocket articles to be imported
	-- 1/10 would, e.g., import the first ten articles you've ever stored in Pocket
	-- 1 and, say, 100000 would presumably move all of them into DT

zachcp / devtools_check.log

Created January 20, 2020 17:49

rCDK build failure 20200120

	* using log directory ‘/private/var/folders/yc/53w8dbxx2hjg11_brr2pj5740000gn/T/RtmpWPpy1T/rcdk.Rcheck’
	* using R version 3.6.0 (2019-04-26)
	* using platform: x86_64-apple-darwin15.6.0 (64-bit)
	* using session charset: UTF-8
	* using options ‘--no-manual --as-cran’
	* checking for file ‘rcdk/DESCRIPTION’ ... OK
	* this is package ‘rcdk’ version ‘3.4.9.2’
	* checking package namespace information ... OK
	* checking package dependencies ... OK
	* checking if this is a source package ... OK

zachcp / npatlas_to_wikidata.clj

Created December 21, 2019 17:54

np-atlas


	(require '[clj-http.client :as client])
	(require '[clojure.data.csv :as csv])
	(require '[clojure.java.io :as io]))
	(require '[mundaneum.query :refer [describe entity label property query stringify-query default-language clojurize-results Clojurizable]])
	(require '[mundaneum.properties :refer [properties]])
	(require '[backtick :refer [template syntax-quote]])


	;; data loading functions

zachcp / count-duplicate-inchis.sparql

Last active December 8, 2019 16:09

Some WikiData Queries

	SELECT (COUNT(*) as ?agg)
	WHERE {
	SELECT (COUNT(*) as ?count)
	WHERE {
	?item wdt:P235 ?inchi .
	SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en" . }
	}
	GROUP BY ?item
	HAVING( COUNT(?inchi) > 1)
	LIMIT 1000