Yosuke Tanigawa yk-tanigawa

## parallel to replace loops
$ 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


## python_environment_set_up.md

      
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    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


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

## configuration

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

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

## myheatmap.py
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()

## file0.txt
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/

## .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

## README
いつも使うpython notebook の最初に書くimport 文

## file0.txt
- 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`

## fasta_parse.py
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:
	## line starting with '#' is will be ignored by your computer (comment line)

	## configuration

	Host nickname_of_your_server
	User somebody@somewhere.com
	Port 22
	Hostname server
	IdentityFile ~/.ssh/server
	IdentitiesOnly yes
	def someMap: Map[String, Int]
	someMap.keys.map(key => (key -> someMap(key).someFunc)).toMap
	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()
	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/
	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
	- 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`