danielecook

function sort_vcf {
    grep "^#" ${1} 
    grep -v "^#" ${1} | sort -V -k1,1 -k2,2n
}

danielecook

Python Versus Nim: Async

• No performance benchmark.
• Python ⟿ PEP-8
• Nim ⟿ NEP1
• Python ⟿ 3.7
• Nim ⟿ 0.19
• No Ofuscation, no Code-Golf.

This is to compare elegant, simple, expressive code.

danielecook

function ls_snapshot {
    if [[ -z $1 ]]; then
        n_backup=1
    else
        n_backup=${1}
    fi;
    search=""
    original_path=$(pwd -P)

danielecook

import scholarly

search_results = scholarly.search_pubs_query("CeNDR")
top = next(search_results)
assert top.bib["title"] == "CeNDR, the Caenorhabditis elegans natural diversity resource"
citations = list(top.get_citedby())

for i in citations:
    print("\t".join(i.bib["title"], i.bib["author"], i.bib.get("eprint"))]

danielecook

# A double bar || OR in R "short circuits"
# The || operator will skip evaluating the second argument if the first argument is TRUE.
{ print("left"); TRUE } || { print("right"); TRUE } # Prints left
{ print("left"); FALSE } || { print("right"); TRUE } # Prints left, right

# The && operator will skip evaluating the second argument if the first argument is TRUE.
{ print("left"); TRUE } && { print("right"); TRUE } # Prints left, right
{ print("left"); FALSE } && { print("right"); TRUE } # Prints right

# Both arguments will be evaluated, even though the first one is TRUE

danielecook

conda activate primary-env

function extract_gts() {
    i=${1}
    patient=$(echo ${i} | egrep -o "LTX[0-9]+" | head -n 1)
    sample=$(echo ${i} | cut -f 5 -d "/")
    vcf2tsv -g ${i} | \
    awk -v patient=${patient} -v fname=${i} -v OFS="\t" -v sample=${sample} 'NR == 1 { print "patient", "sample", "fname", $0 } NR > 1 { print patient, sample, fname, $0 }' | \
    awk '!arr[$0]++' > gl_genotypes/${patient}.tsv
}

danielecook

function excel() {
    tmp=`mktemp`
    out=${1}
    cat ${out} > $tmp
    open -a "Microsoft Excel" $tmp
}

danielecook

#!/usr/bin/env nextflow
@Grab(group='commons-io', module='commons-io', version='2.6')
import org.apache.commons.io.FilenameUtils;

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

uint32.high # High value for uint32
uint32.low # Low value for uint32