Yosuke Tanigawa yk-tanigawa

Yosuke Tanigawa is a Research Scientist at MIT Computational Biology Lab (PI: Prof. Manolis Kellis).

yk-tanigawa / How to access to jupyter notebook at remote

Created January 23, 2016 17:39

	local$ ssh -L 8888:localhost:8888 remote
	remote$ jupyter notebook

yk-tanigawa / jupyter_notebook_config.py

Created January 25, 2016 17:01

	#------------------------------------------------------------------------------
	# Configurable configuration
	#------------------------------------------------------------------------------

	c = get_config()
	#c.NotebookApp.ip = '*'
	c.NotebookApp.password = u'sha1:xxxx'
	c.NotebookApp.open_browser = False
	#c.NotebookApp.port = 8899

yk-tanigawa / Makefile to obtain paired-end FASTQ file

Created February 23, 2016 02:12

	#usage: make SRA=XXXXX.sra

	## commands
	FASTQ-DUMP = /somewhere/fastq-dump

	## files
	FASTQ1 = $(SRA:%.sra=%_1.fastq)
	FASTQ2 = $(SRA:%.sra=%_2.fastq)

	all: $(FASTQ1) $(FASTQ2)

yk-tanigawa / file0.txt

Created February 23, 2016 02:34

NCBI SRA (Short Read Archive) 形式から fastq 形式に変換する Makefile ref: http://qiita.com/yk-tanigawa/items/f78834d697daf23378b0

	## commands
	FASTQ-DUMP = /somewhere/fastq-dump

	## files
	FASTQ1 = $(SRA:%.sra=%_1.fastq)
	FASTQ2 = $(SRA:%.sra=%_2.fastq)

	all: $(FASTQ1) $(FASTQ2)

	# obtain the paired-end fastq files from a given sra file

yk-tanigawa / 20160303BiomartServer.ipynb

Created March 4, 2016 07:19

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yk-tanigawa / fasta_parse.py

Created April 19, 2016 01:35

	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:

yk-tanigawa / file0.txt

Created May 6, 2016 05:32

Scala + Apache Spark をIntelliJにて開発する方法 ref: http://qiita.com/yk-tanigawa/items/4fc86c7e0e529c3b2fa0

	- 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 / README

Created May 12, 2016 02:57

python notebook

いつも使うpython notebook の最初に書くimport 文

yk-tanigawa / .ssh_config

Last active June 21, 2017 18:39

Templates

yk-tanigawa / file0.txt

Last active May 18, 2016 08:51

fasta file のparser snipet ref: http://qiita.com/yk-tanigawa/items/0361b029863fa17e7ed9

	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/