yk-tanigawa

def myheatmap(ndary):
    X, Y = ndary.shape
    fig = plt.figure(figsize=(8,8))
    ax = fig.add_subplot(1,1,1)
    ax.set_xlim(0, Y)
    ax.set_ylim(0, X) 
    ax.invert_yaxis()
    ax.pcolor(ndary, cmap=plt.cm.Blues)
    fig.show()

yk-tanigawa

def someMap: Map[String, Int]
someMap.keys.map(key => (key -> someMap(key).someFunc)).toMap

yk-tanigawa

## line starting with '#' is will be ignored by your computer (comment line)

## configuration

Host nickname_of_your_server
  User [email protected]
  Port 22
  Hostname server
  IdentityFile ~/.ssh/server
  IdentitiesOnly yes

yk-tanigawa

install necessary software to cluster machine

pyenv

• download and install pyenv via github

$ git clone https://github.com/yyuu/pyenv.git ~/.pyenv

• add the following to ~/.bash_profile

yk-tanigawa

$ parallel mkdir -p dirs/{2}/{1} :::: <(seq 1 10) <(seq 1 5)

$ parallel -k  'echo {}' :::: <(seq 1 10)

$ # https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1

yk-tanigawa

#!/bin/sh

# (@) hello world

#SBATCH --job-name=hello
#SBATCH   --output=hello.%j.out
#SBATCH    --error=hello.%j.err
#SBATCH --time=0:01:00
#SBATCH --qos=normal
#SBATCH -p normal

yk-tanigawa

np.array(
        Parallel(
            n_jobs=multiprocessing.cpu_count()
        )(delayed(pre_process_main)(read_3channel_file(lead_df, i))
          for i in range(batch_interval[0], batch_interval[1])),
        dtype = np.float64
    )

yk-tanigawa

$ python pgen_write.py
2017-07-04 00:44:50,706 pgen_write   DEBUG    pgen write test script
2017-07-04 00:44:50,706 read_alleles_range DEBUG    reading alleles range 0:10 from ./pgen_in.pgen
2017-07-04 00:44:50,725 read_alleles_range DEBUG    The shape of the numpy nd-array is (10, 224676)
2017-07-04 00:44:50,725 pgen_write   DEBUG    shape of buffer is (10, 224676)
2017-07-04 00:44:50,727 pgen_write   DEBUG    writing SNP 0 of 10 ...
2017-07-04 00:44:50,728 pgen_write   DEBUG    writing SNP 1 of 10 ...
2017-07-04 00:44:50,730 pgen_write   DEBUG    writing SNP 2 of 10 ...
2017-07-04 00:44:50,731 pgen_write   DEBUG    writing SNP 3 of 10 ...
2017-07-04 00:44:50,733 pgen_write   DEBUG    writing SNP 4 of 10 ...

yk-tanigawa

yk-tanigawa

This script works as a wrapper for sbatch command.

Usage: sherlock-one-liner python --version