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

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

## 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

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

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

from itertools import groupby
import gzip

# Fasta IO
def fasta_iter(fasta_name):
    '''
    given a fasta file. yield tuples of header, sequence
    modified from Brent Pedersen
    Correct Way To Parse A Fasta File In Python
    https://www.biostars.org/p/710/

yk-tanigawa

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

Host *
  ControlMaster auto
  ControlPath ~/.ssh/mux-%r@%h:%p

yk-tanigawa

いつも使うpython notebook の最初に書くimport 文

yk-tanigawa

- 例えば，http://qiita.com/chosan211/items/1472198165442e93047e などを参照してインストールする
- 手元のmac環境の場合は，macports を使って下記のように簡単にインストールできた
    - `$sudo port install maven3`
    - `$sudo port select --set maven maven3`
    - `$ mvn --version`

yk-tanigawa

from itertools import groupby

def fasta_iter(fasta_name):
    '''
    given a fasta file. yield tuples of header, sequence
    modified from Brent Pedersen
    Correct Way To Parse A Fasta File In Python
    https://www.biostars.org/p/710/
    '''
    with open(fasta_name) as f: