KEGG API学习笔记（2）

假设现在有两比较样本的microarray芯片的资料需要分析，资料以列表的形式表示，列表示例如下：

	1_Signal	1_Detection	2_Signal	2_Detection	Descriptions
1771550_at	66.8	P	67.2	A	S. cerevisiae YAL064W-B GEN=SEO1 DB_XREF=GI:6319253 SEG=NC_001133:+12047,12427 DEF=Hypothetical ORF NOTE=Yal064w-bp; go_component: cellular_component unknown [goid GO:0008372] [evidence ND]; go_function: molecular_function unknown [goid GO:0005554] [evidence ND]; go_process: biological_process unknown [goid GO:0000004] [evidence ND]
1772356_at	23.8	A	13.6	A	S. cerevisiae YAL064C-A GEN=SEO1 DB_XREF=GI:7839146 SEG=NC_001133:-13364,13744 DEF=Hypothetical ORF NOTE=Yal064c-ap; go_component: cellular_component unknown [goid GO:0008372] [evidence ND]; go_function: molecular_function unknown [goid GO:0005554] [evidence ND]; go_process: biological_process unknown [goid GO:0000004] [evidence ND]
1772528_at	7.3	A	3.2	A	S. cerevisiae YAL064W GEN=SEO1 DB_XREF=GI:6319254 SEG=NC_001133:+21526,21852 DEF=Hypothetical ORF NOTE=Yal064wp; go_component: cellular_component unknown [goid GO:0008372] [evidence ND]; go_function: molecular_function unknown [goid GO:0005554] [evidence ND]; go_process: biological_process unknown [goid GO:0000004] [evidence ND]
1776321_at	120.9	P	40.3	A	S. cerevisiae YAL063C-A GEN=SEO1 DB_XREF=GI:33438755 SEG=NC_001133:-22397,22687 DEF=Identified by expression profiling and mass spectrometry NOTE=Yal063c-ap; go_component: cellular_component unknown [goid GO:0008372] [evidence ND]; go_function: molecular_function unknown [goid GO:0005554] [evidence ND]; go_process: biological_process unknown [goid GO:0000004] [evidence ND]
1779679_s_at	197.5	P	204.6	P	S. cerevisiae YAL063C GEN=FLO9 DB_XREF=GI:6319255 SEG=NC_001133:-24001,27969 DEF=Lectin-like protein with similarity to Flo1p, thought to be expressed and involved in flocculation NOTE=Flo9p; go_component: cell wall (sensu Fungi) [goid GO:0009277] [evidence ISS] [pmid 7502576]; go_function: mannose binding [goid GO:0005537] [evidence ISS] [pmid 7502576]; go_process: flocculation (sensu Saccharomyces) [goid GO:0000501] [evidence IEP,ISS] [pmid 7502576]

列表中第一列为microarray中的序列编号，第二，四列为信号强度，第三，五列信号可识别度，P为良好，A为差，第六列为信息说明。需要比较两次实验中信号良好的两信号差别，差异显著的，使用KEGG的代谢算途径库图象化表示，并提供统计表，清晰描绘两次实验的差异。

#!/usr/bin/perl
#使用SOAP::Lite
use SOAP::Lite;
#为SOAP准备wsdl参数
$wsdl = 'http://soap.genome.jp/KEGG.wsdl';
#定义指针提供KEGG API接口
$soap_ser = SOAP::Lite->service($wsdl);
 
#定义文件名（包括完整路径）
$filename = "C:\\TPS1NS.xls";
#打开文件，如果打不开中止程序。
open(MICROARRAY, $filename)||die ("Could not open file");
#统计有多少基因上调，有多少基因下调
$up_reg = 0;
$down_reg = 0;
#逐行读取文件
while($line = <MICROARRAY>){
#文件列表分格符为制表符
$pattern = "\x09";
#将读取的一行数据按定义好的分格符分割成字串存在words为名的数组里。
@words = split(/$pattern/, $line);
#选择信号显著的数据进行比较
if ($words[2]=~/P/ && $words[4]=~ /P/){
#计算数值的数量级差别
$ratio=log($words[1])-log($words[3]);
#当数量级差别大于等于1时，对数据进行处理
if(abs($ratio)>=1){
#统计有多少基因上调或者下调表达
if($ratio>=1){
$up_reg += 1;
}
if($ratio<=-1){
$down_reg +=1;
}
#查找字符串以DB_XREF=开头，以空格结束的字串，
#中间的部分，前面的字母将存在$1变量中，后面的数字将存在$2变量中。
if($words[5]=~/DB_XREF=(\D+)(\d+)\s/){
#因为变量$1,$2的作用域有限，所以将它们先存起来。
$db_pre=$1;
$db_id=$2;
#查找microarray当中注释数据库的前缀，不同的生物使用的数据库不同。本例中使用的是NCBI GI数据。
if($db_pre=~/GI/){
#将外部数据库ID转换成KEGG数据库ID
$kegg_id = $soap_ser->bconv("ncbi-gi:$db_id");
#输出结果
print $kegg_id;
}
}
}
}
}
#关闭文件
close(MICROARRAY);
#输出统计结果
print $up_reg." genes up regulated. And ".$down_reg." genes down regulated.";
print "\nThis is the end!";

ncbi-gi:6319269    sce:YAL047C    equivalent
ncbi-gi:6319323    sce:YAR009C    equivalent
ncbi-gi:6319369    sce:YBL100W-B    equivalent
ncbi-gi:6319605    sce:YBR129C    equivalent
ncbi-gi:7839147    sce:YCR024C-A    equivalent
ncbi-gi:6319961    sce:YDL240W    equivalent
ncbi-gi:6320437    sce:YDR231C    equivalent
ncbi-gi:7839158    sce:YDR261W-B    equivalent
ncbi-gi:6320531    sce:YDR324C    equivalent
ncbi-gi:6320656    sce:YDR448W    equivalent
ncbi-gi:6320676    sce:YDR468C    equivalent
ncbi-gi:6320819    sce:YEL017C-A    equivalent
ncbi-gi:6320844    sce:YER007C-A    equivalent
ncbi-gi:6320986    sce:YER138W-A    equivalent
ncbi-gi:14318454    sce:YFL065C    equivalent
ncbi-gi:14318511    sce:YFL010W-A    equivalent
ncbi-gi:6321196    sce:YGL241W    equivalent
ncbi-gi:41629691    sce:YGL201C    equivalent
ncbi-gi:6321656    sce:YGR217W    equivalent
ncbi-gi:6321739    sce:YHL048W    equivalent
ncbi-gi:6321833    sce:YHR043C    equivalent
ncbi-gi:33438808    sce:YHR175W-A    equivalent
ncbi-gi:6322648    sce:YKL201C    equivalent
ncbi-gi:6322758    sce:YKL092C    equivalent
ncbi-gi:6323371    sce:YLR340W    equivalent
ncbi-gi:33438853    sce:YMR030W-A    equivalent
ncbi-gi:6323957    sce:YMR299C    equivalent
ncbi-gi:6324623    sce:YOR049C    equivalent
ncbi-gi:6324767    sce:YOR193W    equivalent
ncbi-gi:6324948    sce:YOR372C    equivalent
31 genes up regulated. And 0 genes down regulated.
This is the end!