skchronicles

#!/usr/bin/env bash

set -euo pipefail

function unique_combinations() {
    # Returns all unique possible combinations
    # of a collection of elements of a given length, 
    # to return all possible unique combinations, 
    # set the last argument equal to the length of 
    # the input collection, see example below: 

skchronicles

#!/usr/bin/env python3

"""md5.py: calculates md5s of multiple files in parallel.

The md5 calculation is memory safe. It reads in a file
in blocks of 64 KiB.

USAGE:
  python3 md5.py file1.txt file2.csv 8

skchronicles

#!/usr/bin/env bash

function err() { cat <<< "$@" 1>&2; }
function fatal() { cat <<< "$@" 1>&2; exit 1; }
function retry() {
  # Tries to run a cmd 5 times before failing 
  # If a command is successful, it will break out of attempt loop
  # Failed attempts are padding with the following exponential 
  # back-off strategy {4, 16, 64, 256, 1024} in seconds
  # @INPUTS "$@"" = cmd to run 

skchronicles

#!/usr/bin/env bash
set -euo pipefail


function usage() { cat << EOF

HERVx: Pipeline to characterize Human Endogenous Retrovirus (HERV) expression

USAGE:
  HERVx.sh [OPTIONS] -r1 SRR4235541_1.fastq -r2 SRR4235541_2.fastq -o outdir_path

skchronicles

from __future__ import print_function, division
import sys, os, re
import pandas as pd

# Configuration for defining valid files, cleaning sample names, parse fields, rename fields
# Add new files to parse and define their specifications below
config = {
    ".warning": ["\033[93m", "\033[00m"], ".error": ["\033[91m", "\033[00m"],

	"multiqc_cutadapt.txt": {

skchronicles

#!/bin/bash

# Functions
download() { echo -e "Saving output to file: $1"; curl --http1.1 --retry 5 --verbose -L 'https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?q=*:*&fq=%7B!tag=SeqType_s%7DSeqType_s:(%22Nucleotide%22)&fq=VirusLineageId_ss:(2697049)&cmd=download&sort=SourceDB_s%20desc,CreateDate_dt%20desc&dlfmt=fasta&fl=id,Definition_s,Nucleotide_seq' > "$1" || echo 'Download failed... please try again!'; }
echoerr() { cat <<< "$@" 1>&2; }
help() { cat << EOF

Download the latest SARS-CoV-2 sequence from GeneBank and RefSeq. Please note that providing 
the output filename of the downloaded sequences is optional. 

skchronicles

#!/bin/bash
set -euo pipefail


help() { cat << EOF
Calculates S3 etag

USAGE:
    s3etag [OPTIONS] input_file [chunk_size_in_MB]

skchronicles

from __future__ import print_function
import pandas as pd
import sys


usage = '''\
USAGE:
    python xlsx_reader.py input.xlsx output_file_prefix [-h]

Positional Arguments:

skchronicles

# USAGE: image2html /path/to/images/*.png > out.html

function image2html(){
    for f in $@; do b=$(cat "$f" | base64 -w 0); echo "<img src=\"data:image/${f##*.};base64,${b}\" alt=\"${f%.*}\">"; done
}

export -f image2html