Martijn Vermaat martijnvermaat

Keybase proof

I hereby claim:

I am martijnvermaat on github.
I am martijnvermaat (https://keybase.io/martijnvermaat) on keybase.
I have a public key ASBU9sNz9RzOg8_nT4dssYbLszQejvkoSlY84KZDTpH_Dwo

To claim this, I am signing this object:

Installation of NixOS with encrypted root

These are my notes on instaling NixOS 16.03 on a Lenovo ThinkPad X1 Carbon (4th generation) with an encrypted root file system using UEFI.

Most of this is scrambled from the following pages:

Genomic GenBank files and transcript identifiers

Using the attached script we check all genomic GenBank files in the server cache for the transcript_id field in their mRNA features.

Using the cache from `mutalyzer.nl`

Category	Files checked	Transcripts	With ID	Without ID	%
`NG_`	3076	5989	5978	11	0.2 %

Quick introduction

Initial screen

When the program is started, the user is presented with a minimal pedigree consisting of a father, a mother and a child. On the left of the screen there is a slider for zooming in and zooming out.

In the top left corner three buttons can be seen, two of them (undo and redo) are greyed out. The third button is for downloading the pedigree.

In the top right corner two buttons can be seen, the left one (drawing view) is

Operational semantics for HGVS

This formalisation is based on the idea that the meaning of a variant description is a set of fixed sequences projected on the referencesequence. (We call them replacements, but they can also be identities.) We explicitely do not mean the result (sequence) of applying these replacements. At least in my understanding, that is not how HGVS is intended to interpreted (and would also make it impossible to combine variants; how do you combine two plain sequences?).

	---
	- hosts: all
	tasks:
	- include_vars: vars_plain.yml
	- assert: that="var == 'vars_plain_yml'"
	- include_vars: vars_vaulted.yml
	- assert: that="var == 'vars_vaulted_yml'"
	- include_vars: vars_plain
	- assert: that="var == 'vars_plain'"
	- include_vars: vars_vaulted

	# Auto SSH session aliases for hosts configured in ~/.ssh/config.
	command_not_found_handle() {
	if [[ ! "$1" ]] ; then
	return 127
	fi
	if ! grep -q "^Host $1\$" ~/.ssh/config; then
	return 127
	fi
	ssh $*
	}

	<!doctype html>
	<style>
	#original input[type=range] {
	-webkit-appearance: none !important;
	}

	#original input[type=range]::-webkit-slider-runnable-track {
	height: 2px;
	width: 100px;
	background: red;

	#!/usr/bin/env python
	"""
	Modification of `python -m SimpleHTTPServer` with a fallback to /index.html
	on requests for non-existing files.

	This is useful when serving a static single page application using the HTML5
	history API.
	"""

	# NCBI36
	wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Homo_sapiens/sequence/BUILD.36.3/initial_release/seq_gene.md.gz -O - \
	\| zcat \| sort -t $'\t' -k 11,11 -k 2,2 > /tmp/hg18.seq_gene.sorted.md
	mutalyzer-admin assemblies import-mapview -a hg18 /tmp/hg18.seq_gene.sorted.md 'reference'
	mutalyzer-admin assemblies import-reference -a hg18 'NC_001807.4'

	# GRCh37
	wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Homo_sapiens/sequence/ANNOTATION_RELEASE.105/initial_release/seq_gene.md.gz -O - \
	\| zcat \| sort -t $'\t' -k 11,11 -k 2,2 > /tmp/hg19.seq_gene.sorted.md
	mutalyzer-admin assemblies import-mapview -a hg19 /tmp/hg19.seq_gene.sorted.md 'GRCh37.p13-Primary Assembly'