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

danielecook

grantham <- readr::read_tsv("https://gist.githubusercontent.com/danielecook/501f03650bca6a3db31ff3af2d413d2a/raw/5583a134b36b60762be6cd54002a0f4044338cd0/grantham.tsv") %>%
  tidyr:: gather(SECOND,SCORE, -FIRST) %>% dplyr::filter(SCORE > 0)  


calculate_grantham <- function(a1, a2) {
  (grantham %>% dplyr::filter(FIRST == a1, SECOND == a2))$SCORE
}

danielecook

"""
Daniel E. Cook 2013 
(danielecook.com)

This script takes a csv containing authors and associated Pubmed identifiers (PMIDs) of their publications and outputs a formatted html document of their publications.
The first row of the csv should contain the authors, and each row below their publications (as PMIDs). If you put something other than a PMID in it will simply be outputted -
so you can add publications that might not be in pubmed or that you want to display in a certain way.

This script might be useful for individuals who maintains publication lists for researchers at a university, for instance. 

danielecook

from pyquery import PyQuery as pq
from icalendar import Calendar, Event
import datetime
from datetime import date, timedelta
from dateutil.relativedelta import *
from dateutil.parser import *
from pprint import pprint as pp

clubid = 722
url = "https://www.lafitness.com/Pages/ClassSchedulePrintVersion.aspx?clubid=%s" % clubid

danielecook

#!/usr/bin/Rscript

#SBATCH --job-name=mops

#SBATCH --output=../log/%j.txt
#SBATCH --error=../log/%j.out

#SBATCH --partition=compute

#SBATCH --nodelist=node3

danielecook

# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples

function bam_chromosomes() {
    # Fetch chromosomes from a bam file
    samtools view -H $1 | \
    grep -Po 'SN:(.*)\t' | \
    cut -c 4-1000
}

danielecook

{
    "cmd": ["/usr/local/var/pyenv/shims/python", "-u", "$file"],
    "file_regex": "^[ ]*File \"(...*?)\", line ([0-9]*)",
    "selector": "source.python"
}

danielecook

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:

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

# Source: https://lh3.github.io/2021/07/06/remapping-an-aligned-bam
samtools collate -Oun128 in.bam | samtools fastq -OT RG,BC - \
  | bwa mem -pt8 -CH <(samtools view -H in.bam|grep ^@RG) ref.fa - \
  | samtools sort -@4 -m4g -o out.bam -