Takao Yokoyama wakuteka

## index.pl
#!/usr/bin/perl
use strict;
use warnings;

my $target="ATcgAGCGTTTCG";

print $target."\n";
$target=uc("ATcgAGCGTTTCG");


## genomeindex.pl
#!/usr/bin/perl
use strict;
use warnings;

my $target="ATcgAGCGTTTCG";
my $line;


open (DATAFILE, " < /home/work/biol/References/hg19/chr2.fa")) or die("error: no such file! \n!);
print $target."\n";

## agqr.rb
# -*- coding: utf-8 -*-
# record AGQR
# usage: use with crontab
# 29,59 * * * sleep 40; ruby agqr.rb

require 'yaml'

rtmpdump = '/usr/local/bin/rtmpdump'
ffmpeg = '/usr/bin/ffmpeg'
agqr_stream_url = 'rtmp://fms-base1.mitene.ad.jp/agqr/aandg22'

## gist:1c1f64b6a98679e14361
$ls -l /etc/systemd/system/default.target
lrwxrwxrwx 1 root root 37  9月  2 22:25 /etc/systemd/system/default.target -> /lib/systemd/system/multi-user.target

## gist:925d7427e0d9d764d503
$ uptime
22:47:36 up 32 min, 1 user, load average: 0.00, 0.01, 0.05

## writeXStringset.R
# パッケージのインストール
source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")

# パッケージのロード
library(Biostrings)

# 読み込むmultifastaファイルの指定(ここでは組み込みのデータを使用)
# 例: inFileName <- "sample.fasta"

## random.R
> library(random)

# 関数が5つしかないシンプルなパッケージです。
> ls("package:random")
[1] "quotaCheck"     "randomNumbers"  "randomQuota"
[4] "randomSequence" "randomStrings"

# randomNumbers()は重複を許した乱数列を生成します。
# runif()とは違い、出力されるのは全てint型の整数です。
> randomNumbers(n=20,min=1,max=100,col=5,base=10,check=TRUE)

## gist:4426129
library(cummeRbund)
packagePath <- system.file(package="cummeRbund")
extdataPath <- paste(packagePath, "/extdata", sep = "")
cuff <- readCufflinks(extdataPath,rebuild=TRUE)

my.fpkmMatrix <- fpkmMatrix(genes(cuff))

plot(x=my.fpkmMatrix$"hESC",
     y=my.fpkmMatrix$"Fibroblasts",
     log="xy",

## gist:4426042
scatter <- csScatter(genes(cuff),"hESC","Fibroblasts",smooth=T)
print(scatter)
p <- ggplot(fpkmMatrix(genes(cuff)), aes(hESC, Fibroblasts))
p + geom_point()

## takousiki2.R
# original in http://d.hatena.ne.jp/syou6162/20080801/1217528370

url <- "http://research.microsoft.com/en-us/um/people/cmbishop/PRML/webdatasets/curvefitting.txt"
curvefitting <- read.csv(file=url, sep=" ",head=F)

colnames(curvefitting)<-c("x","t")


takousiki <- function(n){
	#!/usr/bin/perl
	use strict;
	use warnings;

	my $target="ATcgAGCGTTTCG";

	print $target."\n";
	$target=uc("ATcgAGCGTTTCG");
	# -- coding: utf-8 --
	# record AGQR
	# usage: use with crontab
	# 29,59 * * * sleep 40; ruby agqr.rb

	require 'yaml'

	rtmpdump = '/usr/local/bin/rtmpdump'
	ffmpeg = '/usr/bin/ffmpeg'
	agqr_stream_url = 'rtmp://fms-base1.mitene.ad.jp/agqr/aandg22'
	$ls -l /etc/systemd/system/default.target
	lrwxrwxrwx 1 root root 37 9月 2 22:25 /etc/systemd/system/default.target -> /lib/systemd/system/multi-user.target
	$ uptime
	22:47:36 up 32 min, 1 user, load average: 0.00, 0.01, 0.05
	# パッケージのインストール
	source("http://bioconductor.org/biocLite.R")
	biocLite("Biostrings")

	# パッケージのロード
	library(Biostrings)

	# 読み込むmultifastaファイルの指定(ここでは組み込みのデータを使用)
	# 例: inFileName <- "sample.fasta"
	> library(random)

	# 関数が5つしかないシンプルなパッケージです。
	> ls("package:random")
	[1] "quotaCheck" "randomNumbers" "randomQuota"
	[4] "randomSequence" "randomStrings"

	# randomNumbers()は重複を許した乱数列を生成します。
	# runif()とは違い、出力されるのは全てint型の整数です。
	> randomNumbers(n=20,min=1,max=100,col=5,base=10,check=TRUE)
	library(cummeRbund)
	packagePath <- system.file(package="cummeRbund")
	extdataPath <- paste(packagePath, "/extdata", sep = "")
	cuff <- readCufflinks(extdataPath,rebuild=TRUE)

	my.fpkmMatrix <- fpkmMatrix(genes(cuff))

	plot(x=my.fpkmMatrix$"hESC",
	y=my.fpkmMatrix$"Fibroblasts",
	log="xy",
	scatter <- csScatter(genes(cuff),"hESC","Fibroblasts",smooth=T)
	print(scatter)
	p <- ggplot(fpkmMatrix(genes(cuff)), aes(hESC, Fibroblasts))
	p + geom_point()
	# original in http://d.hatena.ne.jp/syou6162/20080801/1217528370

	url <- "http://research.microsoft.com/en-us/um/people/cmbishop/PRML/webdatasets/curvefitting.txt"
	curvefitting <- read.csv(file=url, sep=" ",head=F)

	colnames(curvefitting)<-c("x","t")



	takousiki <- function(n){