popucui’s gists

popucui / series_matrix2csv.py

Last active November 7, 2024 06:09 — forked from afrendeiro/series_matrix2csv.py

Get a GEO series matrix file describing an experiment and parse it into project level and sample level data.

	#!/usr/bin/env python

	"""
	Get a GEO series matrix file describing an experiment and
	parse it into project level and sample level data.
	"""

	import os
	from typing import Tuple, Union
	import tempfile

popucui / en.conf.ini

Created September 26, 2021 08:43 — forked from Blankwonder/en.conf.ini

	# You can download this config from: http://surge.run/config-example/ios.conf
	# Edit with your computer and copy back to iOS device via iTunes, URL, AirDrop
	# or iCloud Drive
	# Version 2.0

	[General]
	# Log level: warning, notify, info, verbose (Default: notify)
	loglevel = notify
	# Skip domain or IP range. These hosts will not be processed by Surge Proxy.
	# (In macOS version when Set as System Proxy enabled, these hosts will be

popucui / Advanced search Clinvar

Created December 1, 2018 02:38

combination of search terms which can be used in advanced search ClinVar

	## Syntax to use when search ClinVar using chrom:pos style info
	(17[Chromosome]) AND 41244124[Base Position for Assembly GRCh37]

popucui / ansible_user_commands.yml

Created August 10, 2018 07:26

	---
	# this is a demo of how the user commands work and how to reference salted passwords
	# in vars sections. You could also use vars_files if you like (see other examples)

	- hosts: "193"
	remote_user: username
	gather_facts: no
	vars:
	# created with:
	# python -c 'import crypt; print crypt.crypt("This is my Password", "$1$SomeSalt$")'

popucui / ngrok v1 setup

Last active July 6, 2018 02:10

	# refer to this doc for instruction about compiling the ngrok server/client binary
	https://imququ.com/post/self-hosted-ngrokd.html

	# step1_prepare_crt.bash, run this in ngrok directory
	export NGROK_DOMAIN="yourdomain.com"

	/usr/bin/openssl genrsa -out base.key 2048 -config ./openssl.cnf
	/usr/bin/openssl req -new -x509 -nodes -key base.key -days 10000 -subj "/CN=$NGROK_DOMAIN" -out base.pem -config ./openssl.cnf
	/usr/bin/openssl genrsa -out server.key 2048 -config ./openssl.cnf
	/usr/bin/openssl req -new -key server.key -subj "/CN=$NGROK_DOMAIN" -out server.csr -config ./openssl.cnf

popucui / daily_usage_code_tips.bash

Last active September 30, 2018 04:47

	# print 2 line into one
	awk 'NR%2{printf "%s ",$0;next;}1' yourFile
	# copy files using rsync
	rsync -avz -h --progress --files-from=./fastq_list user@host:/ .

	# change password from script
	# this is used not often, yet can be very useful when you need to change passwd from VPS provider's dasgboard
	`echo "newpasswd" \| passwd root --stdin`

	# transform head line to a vector

popucui / Server_maintain_add_user.bash

Last active June 3, 2018 13:24


	# add user "hwang"
	# this method is old way on Ubuntu nowadays, for modern way of doing this, should use "adduser"
	sudo useradd hwang -m -b /data/home -s /bin/bash
	# add to group
	sudo usermod -g dev hwang # For primary group "dev"
	sudo usermod -a -G admin hwang # For secondary group "admin"

	#add new user named "zhangshan"
	sudo useradd zhangsan group001

popucui / Set_rsid_ncbi_variation_services.bash

Last active June 3, 2018 13:13

	# variant_demo_simplify.tsv hold basic info of variant, looks like:
	# chr1 69511 . A G
	# chr1 865694 . C T
	# 1. split input tsv file, cause if records are too many, a server error will be returned,
	## although offical site stat that up to 50000 VCF rows may be posted one time
	# 2. use NCBI variation services API to post all rows which are stored in a file
	split -l 10000 /path/to/variant_demo_simplify.tsv
	for s in $(echo "xa?"); do
	curl -X POST \
	--header "Content-Type: text/plain; charset=utf-8" --header "Accept: text/plain; charset=utf-8" \

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