dceoy

#!/usr/bin/env python

import argparse
import bz2
import gzip
import logging
import os
from pathlib import Path
from pprint import pformat

dceoy

#!/usr/bin/env python

import bz2
import gzip

from Bio import SeqIO


def read_fasta(path):
    if path.endswith('.gz'):

dceoy

#!/usr/bin/env bash
#
# Usage:  ./git_rewind_days.sh <int>

set -eux

DAYS_TO_REWIND="${1}"
COMMIT_DATE=$(git log -1 | sed -ne 's/^Date: \+//p')
REWIDED_DATE=$(date -d "${COMMIT_DATE% *} - ${DAYS_TO_REWIND} days" | awk '{print $1" "$2" "$3" "$4" "$6}')" ${COMMIT_DATE##* }"

dceoy

#!/usr/bin/env bash
#
# https://github.com/dceoy/ansible-dev/blob/master/roles/ruby/files/install_rbenv.sh

set -uex

RBENV_DIR="${HOME}/.rbenv"
RB_BUILD_DIR="${HOME}/.rbenv/plugins/ruby-build"
RBENV="${RBENV_DIR}/bin/rbenv"
[[ ${#} -ge 1 ]] && RB_MAJOR_VER="${1}" || RB_MAJOR_VER=2

dceoy

#!/usr/bin/env bash
#
# https://github.com/dceoy/ansible-dev/blob/master/roles/python/files/install_pyenv.sh

set -uex

PYENV_DIR="${HOME}/.pyenv"
PYENV="${PYENV_DIR}/bin/pyenv"
[[ ${#} -ge 1 ]] && PY_MAJOR_VER="${1}" || PY_MAJOR_VER=3

dceoy

#!/usr/bin/env bash
#
# Usage:  ./install_bio_stack.sh <dest dir path>

set -uex
PREFIX_DIR=$(realpath "${1}")
BIN_DIR="${PREFIX_DIR}/bin"
SRC_DIR="${PREFIX_DIR}/src"

mkdir -p "${SRC_DIR}" "${BIN_DIR}"

dceoy

#!/usr/bin/env python

import subprocess


def run_and_parse_subprocess(**popen_args):
    with subprocess.Popen(**popen_args) as p:
        for line in p.stdout:
            yield line.decode('utf-8')
        if p.poll() == 0:

dceoy

#!/usr/bin/env bash
#
# Usage:  ./install_cudnn.sh <tar file>

set -ex

[[ -n "${1}" ]] \
  && tar -xzvf ${1} -C /tmp \
  && cp /tmp/cuda/include/cudnn.h /usr/local/cuda/include \
  && cp /tmp/cuda/lib64/libcudnn* /usr/local/cuda/lib64 \

dceoy

#!/usr/bin/env python

import numpy as np
from scipy import stats


class HotellingsT2(object):
    def __init__(self, alpha):
        self.anomaly_score_threshold = stats.chi2.ppf(q=(1 - alpha), df=1)

dceoy

#!/usr/bin/env Rscript

if(length(argv <- commandArgs(trailingOnly = TRUE)) > 0) {
  install.packages(pkgs = argv,
                   repos = c(CRAN = 'https://cran.rstudio.com/'),
                   dependencies = TRUE)
} else {
  message('Nothig to do.')
}