[SQL] Query

SELECT *
FROM `u133_best_match_u95_INFO`
WHERE GENE_SYM
IN (

"ARF3", "CCND2", "CHD4", "TXNRD1", "PRKAG1", "CCT2", "CREBL2", "VWF", "ITPR2", "TRAFD1", "TIMELESS", "GPRC5A", "NELL2", "PPFIBP1", "KRAS", "TEAD4", "CLSTN3", "LMO3", "WIF1", "PRH1 ", "TSPAN9", "PTPN11", "PTPRR", "SLC4A8", "KLRA1", "AKAP3","PKP2", "FGF6", "GABARAPL1", "CDKN1B", "IGF1", "OLR1", "GRIN2B", "RAD52", "ANAPC5", "WNK1", "STK38L", "FBXL14", "ACVR1B", "KIAA1467", "EMP1", "MRPS35", "PHLDA1", "FLJ22662", "LEMD3", "IFT81", "NINJ2", "CLEC1A", "TMEM16B", "FAM60A", "CASC1","GALNT8", "MANSC1", "PLEKHA5", "BCL2L14", "TM7SF3", "ARNTL2", "TMTC1", "SCYL2", "BCAT1", "IPO8", "ETV6", "KLHDC5", "FAM80B", "DNM1L", "C12orf35", "TSPAN11", "LOH12CR1", "CACNA2D4", "BICD1", "ATN1", "SVOP", "B4GALNT3", "GPR92", "SRGAP1","AEBP2", "RASSF8", "MGC24039", "SOX5", "CACNA1C", "LRMP", "CMAS", "FGD4", "C12orf51"

)

[R] Array CGH Parse

[R] GLAD package: Gain and Loss Analysis of DNA

source("http://bioconductor.org/biocLite.R") biocLite("GLAD")

Analysis Tool: aCGHtool (http://www.mhh.de/acghtool.html)

library(aCGHtool)

[Perl] 特殊變數

$_	The default input and pattern-searching space.
$digit	Contains the subpattern from a successful parentheses pattern match.
$.	The current input line number of last filehandle read.
$!	Contains the current value of errno.
$0	The name of the file of the Perl script.
@ARGV	The command line arguments issued when the script was started.
@_	The parameter array for subroutines.
%ENV	This associative array contains your current environment.

$_ 就是「這一個變數」，也是所有迴圈會用到的預設變數。

例如要讓perl 印出1到100：

for(1..100){

print $_;

}

$1..$9 這九個特殊變數就是比對的第n個結果

$! 會顯示錯誤的訊息

ex: open(FILE, "test.txt") or die $!;

結果：

沒有此一檔案或目錄 at ./oparse.pl line 32.

若寫成 open(FILE, "test.txt") or die "$!\n";

結果：

沒有此一檔案或目錄

[Perl] mkdir chdir

my $data = <>;

chomp $data;

@dirname = split(/\.fasta/,$data);

mkdir：建立新的目錄 ex: mkdir($dirname[0],0755) || die "$!\n";

chdir：切換目前工作的目錄 ex: chdir($dirname[0]) || die "$!\n";

rename：幫檔案改名

unlink：就像使用rm一樣，unlink可以刪除系統中的某些檔案

[R] install package

以seqLogo為例

http://bioconductor.org/packages/2.2/bioc/html/seqLogo.html

1, 先下載 .tar.gz檔

2. 就 tar檔丟到指定目錄

3. 於該目錄下 key in : R CMD INSTALL seqLogo_1.6.0.tar.gz

4. 即可安裝