zarzen

Table of Contents

• 1. Setup Cpp/C Development Environment in Spacemacs
  • 1.1. 1. Add c/c++ layer
    • 1.1.1. Notes

pthom

Ninja support for CLion IDE

This script enables Ninja-powered builds in CLion IDE by wrapping around CMake, which it uses. See my blog post for details.

Disclaimer

This script is provided AS IS with no guarantees given or responsibilities taken by the author. This script relies on undocumented features of CLion IDE and may lead to instability of build and/or IDE. Use it on your own risk under WTFPL terms.

ryerh

注意：本文内容适用于 Tmux 2.3 及以上的版本，但是绝大部分的特性低版本也都适用，鼠标支持、VI 模式、插件管理在低版本可能会与本文不兼容。

Tmux 快捷键 & 速查表 & 简明教程

启动新会话：

tmux [new -s 会话名 -n 窗口名]

恢复会话：

slowkow

#' Convert counts to transcripts per million (TPM).
#' 
#' Convert a numeric matrix of features (rows) and conditions (columns) with
#' raw feature counts to transcripts per million.
#' 
#'    Lior Pachter. Models for transcript quantification from RNA-Seq.
#'    arXiv:1104.3889v2 
#'    
#'    Wagner, et al. Measurement of mRNA abundance using RNA-seq data:
#'    RPKM measure is inconsistent among samples. Theory Biosci. 24 July 2012.

robphoenix

This is unmaintained, please visit Ben-PH/spacemacs-cheatsheet

Useful Spacemacs commands

• SPC q q - quit
• SPC w / - split window vertically
• SPC w - - split window horizontally
• SPC 1 - switch to window 1
• SPC 2 - switch to window 2
• SPC w c - delete current window

iamalbert

\usepackage{fontspec}   %加這個就可以設定字體
\usepackage{xeCJK}       %讓中英文字體分開設置
\setCJKmainfont{微軟正黑體} %設定中文為系統上的字型，而英文不去更動，使用原TeX字型
\XeTeXlinebreaklocale "zh"             %這兩行一定要加，中文才能自動換行
\XeTeXlinebreakskip = 0pt plus 1pt     %這兩行一定要加，中文才能自動換行

\defaultCJKfontfeatures{AutoFakeBold=6,AutoFakeSlant=.4} %以後不用再設定粗斜
\newCJKfontfamily\Kai{標楷體}       %定義指令\Kai則切換成標楷體
\newCJKfontfamily\Hei{微軟正黑體}   %定義指令\Hei則切換成正黑體
\newCJKfontfamily\NewMing{新細明體} %定義指令\NewMing則切換成新細明體

marcelm

#!/bin/bash
set -euo pipefail
if [ $# -ne 1 -o x$1 == x-h -o x$1 == x--help ]; then
    echo \
"Usage:

    samtools sort -O bam -T prefix ... | bambai BAMPATH

Read a sorted BAM file from standard input, write it to BAMPATH and
index it at the same time (creating BAMPATH.bai)."

gregcaporaso

This depends on biom version >= 2.1.5, < 2.2.0 and vsearch >= 1.7.0.

Please note that all of this is highly experimental. I'm keeping these notes as I work with this approach. For published work, I still recommend using standard pipelines, such as those in QIIME 1.9.1.

$ biom --version
biom, version 2.1.5

$ vsearch --version
vsearch v1.7.0_osx_x86_64, 16.0GB RAM, 8 cores

marcelm

from pysam import AlignmentFile
from pyfaidx import Fasta

def has_mismatch_in_interval(reference, bamfile, chrom, start, end):
    """
    Return whether there is a mismatch in the interval (start, end) in any read mapping to the given chromosome.

    reference -- a pyfaidx.Fasta object or something that behaves similarly
    """
    for column in bamfile.pileup(chrom, start, end):

marcelm

#!/usr/bin/env python3
"""
Running this script is (intended to be) equivalent to running the following Snakefile:

include: "pipeline.conf"  # Should be an empty file

shell.prefix("set -euo pipefail;")

rule all:
    input: