danielecook

rows <- function(tab, idx=TRUE) {
  # Set idx to attach an index column
   if (is.na(tab) || is.null(tab) || nrow(tab) == 0) {
      return(list())
  }
  lapply(seq_len(nrow(tab)), 
         function(i) {
           row <- unclass(tab[i,,drop=F])
           if (idx) {
             row$idx <- i

danielecook

#!/bin/bash
#####################################################
# Name: Bash CheatSheet for Mac OSX
# 
# A little overlook of the Bash basics
#
# Usage:
#
# Author: J. Le Coupanec
# Date: 2014/11/04

danielecook

# Shortcut for going to work directories
# Usage: gw <workdir pattern>
# Replace the work directory below as needed
# Where workdir pattern is something like "ab/afedeu"
function gw {
    path=`ls --color=none -d /path/to/work/directory/$1*`
    cd $path
}

# Go work that fetches work dir from .nextflow.log

andy-thomason

Genomics - A programmer's guide.

Andy Thomason is a Senior Programmer at Genomics PLC. He has been witing graphics systems, games and compilers since the '70s and specialises in code performance.

https://www.genomicsplc.com

Vindaar

Calling Nim from R

A super short introduction how to call Nim code from R using the .C interface. I’m not an R user normally, so I googled and used this post as a reference: https://www.r-bloggers.com/three-ways-to-call-cc-from-r/

Writing our Nim procedure

Let’s define a simple procedure, which we want Nim to do:

elowy01

*bcftools filter
*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

*printing out info for only 2 samples:
bcftools view -s NA20818,NA20819 filename.vcf.gz

*printing stats only for variants passing the filter:
bcftools view -f PASS filename.vcf.gz

sloanlance

jq: JSONL → TSV conversion

What is TSV?

TSV means "tab-separated values". I prefer this format over CSV ("comma-separated values") because it doesn't require as much quoting. Many programs that can use CSV formatted data can also use TSV, although they may need to be explicitly told of the different format if it's not detected automatically.

However, in any of the jq scripts below, "@tsv" can usually be replaced with "@csv" to get CSV output instead.

nevesnunes

#!/usr/bin/env python2.7

"""
Extract title from PDF file.

Dependencies:
    pip install --user unidecode pyPDF PDFMiner

Usage:
    find . -name "*.pdf" | xargs -I{} pdftitle -d tmp --rename {}

stephenturner

// Place your key bindings in this file to overwrite the defaults
[
    // RStudio: Copy lines up/down with alt+cmd+up/down
    {
        "key": "alt+cmd+down",
        "command": "editor.action.copyLinesDownAction",
        "when": "editorTextFocus && !editorReadonly"
    },
    {
        "key": "shift+alt+down",

itdaniher

import numpy as np
import itertools

def rle(x):
    where = np.flatnonzero
    x = np.asarray(x)
    n = len(x)
    if n == 0:
        return np.array([], dtype=int)
    starts = np.r_[0, where(~np.isclose(x[1:], x[:-1], equal_nan=True)) + 1]