tomsing1

# Shell function to subsample to a fixed number of alignments,
# requiring the sambamba and samtools suites to be available.
# see https://www.biostars.org/p/76791/
function SubSample {
  local FACTOR=$(samtools idxstats $1 | cut -f3 | \
    awk -v COUNT=$2 'BEGIN {total=0} {total += $1} END {print COUNT/total}')

  if [[ $FACTOR > 1 ]]
    then
    echo '[ERROR]: Requested number of reads exceeds total read count in' $1 '-- exiting' && exit 1

laggardkernel

There's not a complete hook system designed in Bash when compared with other modern shells. PROMPT_COMMAND variable is used as a hook in Bash, which is equivalent to precmd hook in ZSH, fish_prompt in Fish. For the time being, ZSH is the only shell I've known that has a chpwd hook builtin.

PROMPT_COMMAND

If set, the value is interpreted as a command to execute before the printing of each primary prompt ($PS1).

https://www.gnu.org/savannah-checkouts/gnu/bash/manual/bash.html#Bash-Variables

chpwd Hook in Bash

hyginn

# Author: Boris Steipe (ORCID: 0000-0002-1134-6758)
# License: (c) Author (2019) + MIT
# Date: 2019-01-17

What are MD5 files good for anyway?

I recently contributed to Siegfried Köstlmeier's qrandom package and overlooked to update the package MD5 file. That got me thinking - these files are actually not mentioned in Writing R Extensions, and they are not mentioned in Hadley Wickham's R Packages either. We find them in the wild - but I did not find an explicit source regarding their format. In fact, there is a puzzled post from 2016 by Matthew Lueder on Stack Overflow "What is the MD5 file in R packages used for? How is it generated?" ... and the sole answer on the page misunderstood the question.

hfossli

#!/bin/bash

CLEAR='\033[0m'
RED='\033[0;31m'

function usage() {
  if [ -n "$1" ]; then
    echo -e "${RED}👉 $1${CLEAR}\n";
  fi
  echo "Usage: $0 [-n number-of-people] [-s section-id] [-c cache-file]"

nick3499

fn main() {
  let rng = 0..30;
  let rng_even_cubed = rng.filter(|n| is_even(*n))
                          .map(|n| n * n * n)
                          .collect::<Vec<i32>>();
  println!("{:?}", rng_even_cubed);
}

fn is_even(n: i32) -> bool {
  n % 2 == 0

luiscape

#
#  Original solution via StackOverflow:
#    http://stackoverflow.com/questions/35802939/install-only-available-packages-using-conda-install-yes-file-requirements-t
#

#
#  Install via `conda` directly.
#  This will fail to install all
#  dependencies. If one fails,
#  all dependencies will fail to install.

mcg1969

Conda Proposal: namespaces

Motivation

We would like to position Conda as a language-agnostic package manager, but at present it maintains a distinct bias towards Python. Given its origins this was expected and, frankly, reasonable. Nevertheless, as we begin to use it to subsume other packaging ecosystems, such as CRAN, NPM, Ruby Gems, etc., we are going to want to overcome this history; and one key challenge is to address naming conflicts across platforms.

DarwinAwardWinner

## This will allow you to use dplyr functions with Bioconductor's
## S4Vectors::DataFrame class. They simply call "as.data.frame" on
## DataFrame objects and then pass them to the methods for
## "data.frame". Note that this entails conversion of S4 vector
## columns to primitive vectors. No attempt is made to convert the
## results back to DataFrame, since such a conversion would not
## restore S4 vector columns that were converted to primitive vectors.

library(S4Vectors)
library(dplyr)

davfre

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

earthgecko

#!/bin/bash
# bash generate random alphanumeric string
#

# bash generate random 32 character alphanumeric string (upper and lowercase) and 
NEW_UUID=$(cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 32 | head -n 1)

# bash generate random 32 character alphanumeric string (lowercase only)
cat /dev/urandom | tr -dc 'a-z0-9' | fold -w 32 | head -n 1