Question

这可能不是自我解释，但是，我正在尝试在比较两个文件后创建一个文件。

FILE1.TXT

GO:0016020
GO:0043065
GO:0003713
GO:0007090

File2.txt

Gene1 "GO:0016020,GO:0003713"
Gene2 "GO:0016020,GO:0003713,GO:0007090"
Gene3 "GO:0003713"

Output.txt的

GO:0016020 Gene1
GO:0016020 Gene2
GO:0003713 Gene1
GO:0003713 Gene2
GO:0003713 Gene3
GO:0007090 Gene2

基本上我想打印file1加上找到第一列的第一列。

我试过这段代码：

awk 'FNR==NR{a[FNR]=$1; next}{print a[FNR],$1}' File1.txt File2.txt > output.txt

output.txt如下所示：

GO:0016020 Gene1
GO:0043065 Gene2
GO:0003713 Gene3

我只报告了一个实例。

有人能帮助我吗

Answer 1

使用GNU awk 4. *表示真正的多维数组：

$ cat tst.awk
BEGIN { FS="[ \"]+" }
NR==FNR {
    split($2,a,/,/)
    for (i=1; i in a; i++) {
        genes[a[i]][$1]
    }
    next
}
{
    if ($0 in genes) {
        for (gene in genes[$0]) {
            print $0, gene
        }
    }
}

$ awk -f tst.awk file2 file1
GO:0016020 Gene1
GO:0016020 Gene2
GO:0003713 Gene1
GO:0003713 Gene2
GO:0003713 Gene3
GO:0007090 Gene2

Answer 2

没有多维数组的替代awk解决方案

$ awk 'NR==FNR{a[$2]=$1;next} {for(r in a) if(r~$1) print $1,a[r]}' file2 file1
GO:0016020 Gene2
GO:0016020 Gene1
GO:0003713 Gene2
GO:0003713 Gene1
GO:0003713 Gene3
GO:0007090 Gene2

Answer 3

或者你可以在经过一些操作之后使用Unix“join”。加入还需要排序文件：

sort file1.txt > file1.sort.txt
cat file2.txt|tr -d \"|tr , " "|awk '{for(i=2;i<=NF;++i)print $i,$1}'|sort|join - file1.sort.txt

Answer 4

我知道这个问题是关于awk的，但我已经在php中开发了一个有效的解决方案

<?php
//Read File1.txt to a varaiable
$file1 = file_get_contents("File1.txt");
//Read File2.txt to a varaiable
$file2 = file_get_contents("File2.txt");
//Creates an empty array to hold the Output
$output = array();

//matches all genes on File1.txt
preg_match_all('/GO:\d+/i', $file1, $matches, PREG_PATTERN_ORDER);

//Loop results of genes on File1.txt
foreach($matches[0] as $gene){
    //match gene number for this specific gene in File2
    preg_match_all("/(Gene\d+).*?$gene/i", $file2, $matches2, PREG_PATTERN_ORDER);
    //Loop matches of File2.txt
for ($i = 0; $i < count($matches2[1]); $i++) {
    //add to array output
    array_push($output, $gene." ".$matches2[1][$i]);
}
}

//unique genes
$output = array_unique($output);
//output the unique genes to Output.txt
foreach($output as $sortedGene){
    file_put_contents('Output.txt',$sortedGene."\n", FILE_APPEND);
}
/*
GO:0016020 Gene1
GO:0016020 Gene2
GO:0003713 Gene1
GO:0003713 Gene2
GO:0003713 Gene3
GO:0007090 Gene2
*/

比较两个文件，在第二个文件中打印每个模式

4 个答案: