Question

亲爱的stackoverflow社区，

我有一个2列的文件，如下所示：

Ccrux.00013.c0_g1_i1    .
Ccrux.00013.c0_g2_i1    .
Ccrux.00014.c0_g1_i1    .
Ccrux.00014.c0_g2_i1    .
Ccrux.00015.c0_g1_i1    .
Ccrux.00015.c0_g1_i1    GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0016021^cellular_component^integral component of membrane`GO:0005509^molecular_function^calcium ion binding`GO:0005506^molecular_function^iron ion binding`GO:0031418^molecular_function^L-ascorbic acid binding`GO:0016706^molecular_function^oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors`GO:0045646^biological_process^regulation of erythrocyte differentiation
Ccrux.00015.c0_g2_i1    GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0016021^cellular_component^integral component of membrane`GO:0005509^molecular_function^calcium ion binding`GO:0005506^molecular_function^iron ion binding`GO:0031418^molecular_function^L-ascorbic acid binding`GO:0016706^molecular_function^oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors`GO:0045646^biological_process^regulation of erythrocyte differentiation
Ccrux.00016.c0_g1_i1    .
Ccrux.00016.c0_g2_i1    .
Ccrux.00017.c0_g1_i1    .
Ccrux.00018.c0_g1_i1    .
Ccrux.00019.c0_g1_i1    .

我需要一个新的2列文件：

不包含第二列值所在的行。
仅包含GO：XXXXXXX作为第二列值（即从第二列中删除所有文本并仅保留GO编号）

新文件应如下所示：

Ccrux.00015.c0_g1_i1    GO:0005789,GO:0016021,GO:0005509,GO:0005506,GO:0031418,GO:0016706,GO:0045646
Ccrux.00015.c0_g2_i1    GO:0005789,GO:0016021,GO:0005509,GO:0005506,GO:0031418,GO:0016706,GO:0045646
Ccrux.00029.c0_g1_i1    GO:0035869,GO:0005737,GO:0005615,GO:0016020,GO:0021956,GO:0060271,GO:0021904,GO:0001701,GO:0001841,GO:0008589,GO:0021523,GO:0021537

我一直在尝试使用perl：

perl -ne '/(GO:\d+)/ && print "$1"' input.file > output.file

但是只在一列中打印出所有GO号码。我真的迷失了怎么做。任何建议都将受到欢迎。

提前谢谢大家。

Answer 1

你有什么模式匹配一段文字，然后打印出来。

你正在做的听起来：

GO:0005789^cellular_component^endoplasmic reticulum membrane`

您是否尝试删除^与下一个GO之间的任何“位”？

perl的好处是语法-ne只是在命令周围创建一个while循环 - 所以它会让你做多个语句。

所以 - 扩展的例子：

#!/usr/bin/env perl 
use strict;
use warnings;

while (<DATA>) {
    next unless m/GO/;
    s/\^[^`]+`/,/g;
    s/\^[^`]+$/\n/g;
    print;
}

__DATA__
Ccrux.00013.c0_g1_i1    .
Ccrux.00013.c0_g2_i1    .
Ccrux.00014.c0_g1_i1    .
Ccrux.00014.c0_g2_i1    .
Ccrux.00015.c0_g1_i1    .
Ccrux.00015.c0_g1_i1    GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0016021^cellular_component^integral component of membrane`GO:0005509^molecular_function^calcium ion binding`GO:0005506^molecular_function^iron ion binding`GO:0031418^molecular_function^L-ascorbic acid binding`GO:0016706^molecular_function^oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors`GO:0045646^biological_process^regulation of erythrocyte differentiation
Ccrux.00015.c0_g2_i1    GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0016021^cellular_component^integral component of membrane`GO:0005509^molecular_function^calcium ion binding`GO:0005506^molecular_function^iron ion binding`GO:0031418^molecular_function^L-ascorbic acid binding`GO:0016706^molecular_function^oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors`GO:0045646^biological_process^regulation of erythrocyte differentiation
Ccrux.00016.c0_g1_i1    .
Ccrux.00016.c0_g2_i1    .
Ccrux.00017.c0_g1_i1    .
Ccrux.00018.c0_g1_i1    .
Ccrux.00019.c0_g1_i1    .

这将生成输出：

Ccrux.00015.c0_g1_i1    GO:0005789,GO:0016021,GO:0005509,GO:0005506,GO:0031418,GO:0016706,GO:0045646
Ccrux.00015.c0_g2_i1    GO:0005789,GO:0016021,GO:0005509,GO:0005506,GO:0031418,GO:0016706,GO:0045646

我们：

跳过任何没有单词GO的行。
用逗号替换文字^的任何实例，一个或多个不是^，然后反引号。
并替换在\n行末尾终止的内容。

这样我们就可以凝聚成一个衬里：

perl -ne 'next unless m/GO/;s/\^[^`]+`/,/g;s/\^[^`]+$/\n/g;print' inputfile > outputfile

或者更好 - 如果不打印 - 请参阅perlrun - -p与-n类似，但它会在print中构建（因此更像{{} 1}}）。

sed

Answer 2

我认为您的要求对于单线解决方案来说有点太长了，但它可以非常简短。该程序将生成您描述的输出。它期望输入文件的路径作为命令行上的参数

use strict;
use warnings;

while ( <> ) {
    next unless my @values = /GO:\d+/g;
    local $" = ',';
    s/\S\s+\K.+/@values/;
    print;
}

单行版本会有点笨重

perl -pe '@v=/GO:\d+/g or next; $"=","; s/\S\s+\K.+/@v/; print;' myfile > newfile

如何从列中提取一些文本以创建新列

2 个答案: