Yixf-Self

#!/usr/bin/python
"""
%prog [options] pair_1.fastq pair_2.fastq

filter reads from paired fastq so that no unmatching reads remain.
output files are pair_1.fastq.trim and pair_2.fastq.trim
see: http://hackmap.blogspot.com/2010/09/filtering-paired-end-reads-high.html
"""
from subprocess import Popen, PIPE
import sys

Yixf-Self

# Generate digitial clock face
first.nine <- c('00', '01', '02', '03', '04', '05', '06', '07', '08', '09')
hours <- c(first.nine, as.character(seq(10,23,1)))
mins <- c(first.nine, as.character(seq(10,59,1)))
time.chars.l <- lapply(hours, function(h) paste(h, ':', mins, sep=''))
time.chars <- do.call(c, time.chars.l)

# Generate analog clock face
hour.pos <- seq(0, 12, 12/(12*60))[1:720]
min.pos <-seq(0,12, 12/60)[1:60]

Yixf-Self

Automation for the People

Long ago, the first time I read "The Pragmatic Programmer", I read some advice that really stuck with me.

"Don't Use Manual Procedures".

This in the chapter on Ubiquitous Automation. To summarize, they want you to automate all the things.

The trouble was that I hadn't much of an idea how to actually go

Yixf-Self

环境 (Environment)

版本：Ubuntu 14.04 LTS 默认语言：English(United States)

安装 (Setup)

Debian 和 Ubuntu 下对中文支持比较好的字体有： fonts-droid、ttf-wqy-zenhei 和 ttf-wqy-microhei 等，除了文泉驿系列字体外，比较流行的免费中文字体还有文鼎提供的楷体和上海宋，包名分别是： fonts-arphic-ukai 和 fonts-arphic-uming。

Yixf-Self

# commands to ignore
cmdignore=(htop tmux top vim)

# end and compare timer, notify-send if needed
function notifyosd-precmd() {
	retval=$?
    if [[ ${cmdignore[(r)$cmd_basename]} == $cmd_basename ]]; then
        return
    else
        if [ ! -z "$cmd" ]; then

Yixf-Self

function active-window-id {
    echo `xprop -root | awk '/_NET_ACTIVE_WINDOW\(WINDOW\)/{print $NF}'`
}

# end and compare timer, notify-send if needed
function notifyosd-precmd() {
    if [ ! -z "$cmd" ]; then
        cmd_end=`date +%s`
        ((cmd_time=$cmd_end - $cmd_start))
    fi

Yixf-Self

==========================================          ==========================================
             TMUX COMMAND                                        WINDOW (TAB)
==========================================          ==========================================

List    tmux ls                                     List         ^b w
New          -s <session>                           Create       ^b c
Attach       att -t <session>                       Rename       ^b , <name>
Rename       rename-session -t <old> <new>          Last         ^b l               (lower-L)
Kill         kill-session -t <session>              Close        ^b &

Yixf-Self

tmux Reference

Creating Sessions

Command	Description
tmux new-session	Create new session without a name. (Alt: tmux or tmux new)
tmux new -s development	Creates new session called "development."
tmux new -s development -n editor	Create new session called "development" and a first window called "editor."
tmux attach -t development	Attaches to a session called "development."

Yixf-Self

itan <- function(x, keys=NULL, digits=3, no.resp=4) {
  # x is an n subjects by k items matrix
  # keys is a vector with the correct keys (A, B, C, D)
  stopifnot(ncol(x)>1)
  if (is.null(keys)) keys <- rep("A", ncol(x))
  require(ltm)
  raw.resp <- matrix(nr=ncol(x), nc=no.resp)
  colnames(raw.resp) <- LETTERS[1:no.resp]
  for (i in 1:ncol(x)) {
    tmp <- table(x[,i])

Yixf-Self

Mode <- function(x) {
     ux <- unique(x)
     ux[which.max(tabulate(match(x, ux)))]
 }