Templates

.ssh_config

Host github.com
  User somebody@somewhere.com
  Port 22
  Hostname github.com
  IdentityFile ~/.ssh/github
  IdentitiesOnly yes

Host *
  ControlMaster auto
  ControlPath ~/.ssh/mux-%r@%h:%p
  GSSAPIAuthentication no
  Compression yes
  CompressionLevel 9
  Cipher arcfour256
  ForwardAgent yes
  TCPKeepAlive               yes
  ServerAliveInterval        15
  ServerAliveCountMax        3
  PasswordAuthentication no

make_hist.py

def make_hist(x, title = None, xlabel = None, ylabel = None, filename = None):
    '''
    This function generates histogram of a vector x and save to file
    Inputs:
      x: data vector
      title:    title of the plot
      xlabel:   label on x-axis
      ylabel:   label on y-axis
      filename: name of the image file (if given, save to file)
    Returns:
      matlab plot object
    Side effect:
      save an image file if filename is given
    '''
    
    import matplotlib
    matplotlib.use('agg')
    from matplotlib import pyplot as plt
    
    fig = plt.figure(figsize=(8,6))
    ax = fig.add_subplot(1, 1, 1)
    ax.hist(x, 20)
    
    if(xlabel != None):
        ax.set_xlabel(xlabel)
    if(ylabel != None):
        ax.set_ylabel(ylabel)
    if(title != None):
        ax.set_title(title)
    if(filename != None):
        fig.savefig(filename)
    
    return(fig)

plot_grid.py

%matplotlib inline


import numpy as np
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
import itertools as it

font = {#'family' : 'normal',
        #'weight' : 'bold',
        'size'   : 20}

matplotlib.rc('font', **font)

fig_conf_curves = plt.figure(figsize=(12, 7))
gs_conf_curves = gridspec.GridSpec(1, 2)
axs = [fig_conf_curves.add_subplot(ss) for ss in gs_conf_curves]
for i in range(10):
    axs[0].plot(conf_curves[i, :, 0], conf_curves[i, :, 1])
    axs[1].plot(conf_curves[i, :26, 0], conf_curves[i, :26, 1])
for ax in axs:
    ax.set_xlabel('conservation bin')
axs[0].set_ylabel('BBL')
axs[0].set_title('conservation bin [0, 100]')
axs[1].set_title('conservation bin [0, 25]')
fig_conf_curves.suptitle(#
"""Confidence curves in 10 different sets of shuffle motifs
B_Atf1_primary, 10 * 10 shuffles, p_value_cutoff=1.3
"""
)
gs_conf_curves.tight_layout(fig_conf_curves, rect=[0, 0, 1, 0.88])
fig_conf_curves.savefig('./compareConfidenceCurves_B_Atf1_primary_curve.png')

pyplot.py

def set_plt_style(n):
    colors = sns.husl_palette(n)
    markers = ['o', 'v', '^', '<', '>', '8', 's', 'p', '*', 'h', 'H', 'D', 'd'] * (int(n / 13) + 1)
    linestyles = ['-', ':', '-.', '--', ':', '-.', '--'] * (int(n / 7) + 1)
    return({'color': colors,
            'marker': markers,
            'linestyle': linestyles})

python_20170227.py

%matplotlib inline

import numpy as np
import scipy as sc
import pandas as pd
import itertools as it
import subprocess as sp
import colorlog
import sys
import re
import collections
import json
import enum
import bisect
import matplotlib
matplotlib.use('agg')
from matplotlib import pyplot as plt


logger = colorlog.getLogger()
logger.setLevel(colorlog.colorlog.logging.DEBUG)
handler = colorlog.StreamHandler()
handler.setFormatter(colorlog.ColoredFormatter())
logger.addHandler(handler)

logger.debug("Debug message")
logger.info("Information message")
logger.warning("Warning message")
logger.error("Error message")
logger.critical("Critical message")

sample.sh

#!/bin/bash
set -beEu -o pipefail

# (@) some comments

tmpRoot=/dev/shm

# Create a temp working dir. This dir will be automatically deleted.
tmpDir=$(mktemp -d -p $tmpRoot)
echo "tmpDir is $tmpDir"
handler_exit () { rm -rf $tmpDir ; }
trap handler_exit EXIT

scatter.py

import matplotlib.pyplot as plt

color = ['red', 'green', 'blue']
legend_loc = 'lower right'
label = ['red', 'green', 'blue']

# prepare matlabplt object
fig = plt.figure(figsize=(16,12))
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)

# define plot region
ax.set_xlim(XMIN, XMAX)
ax.set_ylim(YMIN, YMAX)

# make a scatter plot
for j in xrange(CATEG_NUM):
    ax.scatter(X_j,
               Y_j,
               c = color[j],
               label = label(j))

# show legend
ax.legend(loc=legend_loc)

# return the object
return(plt)

template.pl

#!/usr/bin/env perl

use 5.014;
use utf8;
use warnings;
use diagnostics;                                                                                                                                                                                   
use strict;

use Getopt::Long qw(:config posix_default no_ignore_case gnu_compat);

my ($in_file, $out_file, $param);
GetOptions(
    "input|i=s"  => \$in_file,
    "output|o=s" => \$out_file,
    "param|p=i"  => \$param
);

template.py

%matplotlib inline
import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import pandas as pd
from scipy import io
import math


sns.set_style("ticks")
sns.set_context("paper", font_scale=2.0)


import argparse

def main():
    parser = argparse.ArgumentParser(description='test program')

    parser.add_argument('--version', action='version', version='%(prog)s 20XX-XX-XX')
    parser.add_argument('-o', metavar = 'o', default = None,
                        help = 'output file')
    parser.add_argument('-p', metavar = 'p', type=float,default = 0.001,
                        help = 'param (default: 0.001)')
    args = parser.parse_args()

    print(args.O)

if __name__ == '__main__':
    main()

template.sh

#!/bin/sh

# Mail at end/on suspension
#$ -m es

#$ -S /bin/sh
#$ -cwd
#$ -V
#$ -q all.q

##################################################                                                                                          
# make a copy of this script                                                                                                                
##################################################                                                                                          
cat $0 > "${SGE_O_WORKDIR}/${JOB_NAME}.s${JOB_ID}"

echo hello

#################################

template.tex

\documentclass{article}
\usepackage{amsmath}
\usepackage{amssymb} 
\usepackage{amsfonts}
\usepackage{bm}
\usepackage[dvips]{graphicx}
\usepackage[top=30truemm,bottom=30truemm,left=30truemm,right=30truemm]{geometry}
\begin{document}
\includegraphics[width = \linewidth, bb=0 0 10 10]{hoge.jpg}
\end{document}