martijnvermaat

#!/bin/bash
# Generate a self-signed x509 certificate or certificate signing request and
# key using OpenSSL. DNS and IP addresses can be added as subjectAltName
# entries.
#
# Usage:
#   ./gencert.sh <common name (or DNS name)> <DNS names or ip addresses...> [--rsa4096] [--csr]
#
# By default, a 2048 bits RSA key is generated. Supply --rsa4096 at the end to
# generate a 4096 bits key.

martijnvermaat

# 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'

martijnvermaat

---
- 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

martijnvermaat

Emacs notes

Just some Emacs things that I cannot seem to remember without writing them down. I'm an Emacs newbie (but have been using it for 15 years).

These are random and specific to my setup, so probably not useful to anyone else.

Config can be found here: https://github.com/martijnvermaat/dotfiles

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:

martijnvermaat

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?).

martijnvermaat

Rename plink SNPs to their dbSNP rs id

Download a dbSNP database from the UCSC as a CSV file: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

For example:

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp137Common.txt.gz

Note that the chromStart column values are 0-based.

martijnvermaat

# 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 $*
}

martijnvermaat

Default Vagrant configurations.

Application	IP	SSH forward	HTTP forward	HTTPS forward
Mutalyzer	192.168.111.222	2522	8088	8089
Base server	192.168.111.223	2523
Varda	192.168.111.224	2524	8090	8091
ELK	192.168.111.225	2525	8092	8093
logstash-forwarder	192.168.111.226	2526
Jenkins	192.168.111.227	2527	8094

martijnvermaat

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 %