paniq

max(-x,-y) = -min(x,y)
min(-x,-y) = -max(x,y)

abs(x) = abs(-x)
abs(x) = max(x,-x) = -min(x,-x)
abs(x*a) = if (a >= 0) abs(x)*a
              (a <  0) -abs(x)*a

// basically any commutative operation
min(x,y) + max(x,y) = x + y

Earnestly

A Brief Tour of the Makepkg Process: What Makes a Pacman Package

Introduction

This is a terse document covering the anatomy of a package built for the pacman package manager.

The following example commands can mostly run verbatim to manually create a

jlln

def splitDataFrameList(df,target_column,separator):
    ''' df = dataframe to split,
    target_column = the column containing the values to split
    separator = the symbol used to perform the split

    returns: a dataframe with each entry for the target column separated, with each element moved into a new row. 
    The values in the other columns are duplicated across the newly divided rows.
    '''
    def splitListToRows(row,row_accumulator,target_column,separator):
        split_row = row[target_column].split(separator)

slowkow

#!/usr/bin/env bash
# sra-paired.sh
# Kamil Slowikowski
# April 23, 2014
#
# Check if an SRA file contains paired-end sequencing data.
#
# See documentation for the SRA Toolkit:
# http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump

karenyyng

Title: Tmux project sessions
Date: 2014-12-24 17:00 Tags: Tmux, learn-X-in-Y-minutes
Author: K. Y. Ng

This is a tutorial for setting up Tmux for saving terminal project sessions.

Tmux helps you emulate several shell sessions within the same terminal window.

codemedic

QTabBar,
QTabBar::tab
{
    font-family: "Noto Sans";
    font-size: 11px;
    height: 16px;
    padding: 2px;
    border: 0px;
    border-bottom: 3px solid palette(dark);
    background-color: palette(dark);

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:

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):

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

#!/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)."