viklund

#!perl6

# A lot of the subs in this one can be simplified and merged

class For { 
    has $.value;
    method perl { "For.new('$.value')" }
}

class If {

viklund

cc -o perl6.o -I/home/viklund/proto-2009-06-02/rakudo/parrot/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN  -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHASATTRIBUTE_CONST  -DHASATTRIBUTE_DEPRECATED  -DHASATTRIBUTE_MALLOC  -DHASATTRIBUTE_NONNULL  -DHASATTRIBUTE_NORETURN  -DHASATTRIBUTE_PURE  -DHASATTRIBUTE_UNUSED  -DHASATTRIBUTE_WARN_UNUSED_RESULT  -falign-functions=16 -fvisibility=hidden -funit-at-a-time -maccumulate-outgoing-args -W -Wall -Waggregate-return -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wdisabled-optimization -Wendif-labels -Wextra -Wformat -Wformat-extra-args -Wformat-nonliteral -Wformat-security -Wformat-y2k -Wimplicit -Wimport -Winit-self -Winline -Winvalid-pch -Wlogical-op -Wmissing-braces -Wmissing-field-initializers -Wno-missing-format-attribute -Wmissing-include-dirs -Wpacked -Wparentheses -Wpointer-arith -Wreturn-type -Wsequence-point -Wno-shadow -Wsign-compare -Wstrict-aliasing -Wstrict-aliasing=2 -Wswitch -Wswitch-default -Wtrigraphs -Wundef -Wunkno

viklund

#!/home/johan/perl6/rakudo/perl6

sub unescape($s is rw) {
    my $string = $s;
    $string .= subst('+', ' ', :g);
    # RAKUDO: This could also be rewritten as a single .subst :g call.
    #         ...when the semantics of .subst is revised to change $/,
    #         that is.
    while $string ~~ /\%(<[0..9A..F]>**2)/ {
        my $match = $0;

viklund

use v6;

multi infix:<compress> ( $a, $b ) { $a      ~~ $b ?? $a !! [ $a, $b ] }
multi infix:<compress> ( @a, $b ) { @a[*-1] ~~ $b ?? @a !! [ @a, $b ] }

say ([compress] <a a a a b c c a a d e e e e>).perl;

viklund

use v6;

enum TG <B C D>;

class A { }

my $a1 = A.new( ) but B;
my $a2 = A.new( ) but C;

for $a1, $a2 {

viklund

May-31 05:24:56.746 [main] DEBUG nextflow.cli.Launcher - $> /home/vagrant/bin/nextflow run hello
May-31 05:24:56.813 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.19.2
May-31 05:24:57.037 [main] DEBUG nextflow.scm.AssetManager - Listing projects in folder: /home/vagrant/.nextflow/assets
May-31 05:24:57.042 [main] INFO  nextflow.cli.CmdRun - Pulling nextflow-io/hello ...
May-31 05:24:57.043 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nextflow-io/hello/contents/nextflow.config
May-31 05:24:58.247 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nextflow-io/hello/contents/main.nf
May-31 05:24:58.797 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nextflow-io/hello
May-31 05:24:58.943 [main] DEBUG nextflow.scm.AssetManager - Pulling nextflow-io/hello -- Using remote clone url: https://github.com/nextflow-io/hello.git
May-31

viklund

$ awk '$4>50 && $3>90 && F[$1]++ < 1{print}' blast_result

$4 is column 4 i.e. length, larger than 50bp

$3 percent identity bigger than 90

F[$1]++ < 1 is the tricky part. We count upwards for each query we find and as long as the number
is less than 1 it is true, since the ++ is after the F[$1] the value will be zero the first time
and 1 the second time and so on.

viklund

#!/usr/bin/env ruby
require 'octokit'
require 'set'

def repo_name(repo)
    return ORG + "/" + repo[:name]
end

ORG = "NBISweden"

viklund

import markovify
import json
import os

users = json.load(open('slack/users.json'))

user = ''
for u in users:
    if u['name'] == 'viklund':
        user = u['id']

viklund

#!/bin/bash

MYSQL_PORT=3366
MYSQL_HOST=127.0.0.1
MYSQL_PASS=rootpw

# Start a mysql instance with docker for example like this:
docker volume create swefreq-mysql-data
docker run -v swefreq-mysql-data:/var/lib/mysql --rm --name mysql -e MYSQL_ROOT_PASSWORD=$MYSQL_PASS -d -p $MYSQL_PORT:3306  mysql