awk -在列中找到确切的字符串

Question

我想在一列中找到特定的字符串和字符串的组合。你能帮帮我吗？

投入：

benign,likely_pathogenic
benign,likely_pathogenic
benign,conflicting_interpretations_of_pathogenicity
benign,conflicting_interpretations_of_pathogenicity
benign,conflicting_interpretations_of_pathogenicity
risk_factor,uncertain_significance,likely_pathogenic,uncertain_significance,_other,benign
risk_factor,uncertain_significance,likely_pathogenic,uncertain_significance,_other,benign
risk_factor,benign,likely_benign,drug_response,not_provided,uncertain_significance,pathogenic,uncertain_significance,_other,conflicting_interpretations_of_pathogenicity
pathogenic,not_provided,benign,likely_pathogenic,likely_benign,risk_factor
likely_benign,conflicting_interpretations_of_pathogenicity
benign,likely_benign,conflicting_interpretations_of_pathogenicity
benign,likely_pathogenic
uncertain_significance,likely_benign,conflicting_interpretations_of_pathogenicity
benign,likely_pathogenic
conflicting_interpretations_of_pathogenicity,_other,benign,pathogenic,likely_benign,conflicting_interpretations_of_pathogenicity
conflicting_interpretations_of_pathogenicity,_other,benign,pathogenic,likely_benign,conflicting_interpretations_of_pathogenicity
risk_factor,benign,likely_benign,drug_response,not_provided,uncertain_significance,pathogenic,uncertain_significance,_other,conflicting_interpretations_of_pathogenicity
pathogenic,likely_pathogenic
uncertain_significance,conflicting_interpretations_of_pathogenicity,likely_benign
benign,conflicting_interpretations_of_pathogenicity
benign,conflicting_interpretations_of_pathogenicity
benign,conflicting_interpretations_of_pathogenicity
pathogenic

产出：

benign,likely_pathogenic
benign,likely_pathogenic
risk_factor,uncertain_significance,likely_pathogenic,uncertain_significance,_other,benign
risk_factor,uncertain_significance,likely_pathogenic,uncertain_significance,_other,benign
risk_factor,benign,likely_benign,drug_response,not_provided,uncertain_significance,pathogenic,uncertain_significance,_other,conflicting_interpretations_of_pathogenicity
pathogenic,not_provided,benign,likely_pathogenic,likely_benign,risk_factor
benign,likely_pathogenic
benign,likely_pathogenic
conflicting_interpretations_of_pathogenicity,_other,benign,pathogenic,likely_benign,conflicting_interpretations_of_pathogenicity
conflicting_interpretations_of_pathogenicity,_other,benign,pathogenic,likely_benign,conflicting_interpretations_of_pathogenicity
pathogenic,likely_pathogenic
pathogenic

我想把包含致病性和likely_pathogenic的每一栏分开。但有一部分是在conflicting_interpretations_of_pathogenicity.中引起的。我试过了

awk -F'\t' -v OFS="\t" '{if($14=="pathogenic") print FILENAME,$0; else if($14=="likely_pathogenic") print FILENAME,$0}' 

但它用于列中的确切字符串。

如果我试过：

awk -F'\t' -v OFS="\t" '{if($14~"pathogenic") print FILENAME,$0}'

我得到了所有关于致病性，likely_pathogenic和conflicting_interpretations_of_pathogenicity.的行一排可能是冲突的组合..。致病性或likely_pathogenic。

Answer 1

就像这样，也许：

awk '{
    split($0,a,/,/)                          # split NEEDED field on commas
    for(i in a)                              # check each part
        if(a[i]~/^(likely_)?pathogenic$/) {  # if matches this regex
            print                            # output
            break                            # no need for more matches
        }
}' file

一些产出：

benign,likely_pathogenic
benign,likely_pathogenic
risk_factor,uncertain_significance,likely_pathogenic,uncertain_significance,_other,benign
...

显然，您需要添加FS等，就像在处理NF==14的示例代码中一样。

编辑：

我想这也适用于发布的样本数据：

$ awk '/(^|,)(likely_)?pathogenic(,|$)/' file

或者你的假设数据：

$ awk '$14~/(^|,)(likely_)?pathogenic(,|$)/' file

Answer 2

我将利用GNU AWK的字界来完成这项任务，如下所示，让file.txt内容成为

benign,likely_pathogenic
benign,likely_pathogenic
benign,conflicting_interpretations_of_pathogenicity
benign,conflicting_interpretations_of_pathogenicity
benign,conflicting_interpretations_of_pathogenicity
risk_factor,uncertain_significance,likely_pathogenic,uncertain_significance,_other,benign
risk_factor,uncertain_significance,likely_pathogenic,uncertain_significance,_other,benign
risk_factor,benign,likely_benign,drug_response,not_provided,uncertain_significance,pathogenic,uncertain_significance,_other,conflicting_interpretations_of_pathogenicity
pathogenic,not_provided,benign,likely_pathogenic,likely_benign,risk_factor
likely_benign,conflicting_interpretations_of_pathogenicity
benign,likely_benign,conflicting_interpretations_of_pathogenicity
benign,likely_pathogenic
uncertain_significance,likely_benign,conflicting_interpretations_of_pathogenicity
benign,likely_pathogenic
conflicting_interpretations_of_pathogenicity,_other,benign,pathogenic,likely_benign,conflicting_interpretations_of_pathogenicity
conflicting_interpretations_of_pathogenicity,_other,benign,pathogenic,likely_benign,conflicting_interpretations_of_pathogenicity
risk_factor,benign,likely_benign,drug_response,not_provided,uncertain_significance,pathogenic,uncertain_significance,_other,conflicting_interpretations_of_pathogenicity
pathogenic,likely_pathogenic
uncertain_significance,conflicting_interpretations_of_pathogenicity,likely_benign
benign,conflicting_interpretations_of_pathogenicity
benign,conflicting_interpretations_of_pathogenicity
benign,conflicting_interpretations_of_pathogenicity
pathogenic

然后

/pathogenic\y/{print}

给予输出

benign,likely_pathogenic
benign,likely_pathogenic
risk_factor,uncertain_significance,likely_pathogenic,uncertain_significance,_other,benign
risk_factor,uncertain_significance,likely_pathogenic,uncertain_significance,_other,benign
risk_factor,benign,likely_benign,drug_response,not_provided,uncertain_significance,pathogenic,uncertain_significance,_other,conflicting_interpretations_of_pathogenicity
pathogenic,not_provided,benign,likely_pathogenic,likely_benign,risk_factor
benign,likely_pathogenic
benign,likely_pathogenic
conflicting_interpretations_of_pathogenicity,_other,benign,pathogenic,likely_benign,conflicting_interpretations_of_pathogenicity
conflicting_interpretations_of_pathogenicity,_other,benign,pathogenic,likely_benign,conflicting_interpretations_of_pathogenicity
risk_factor,benign,likely_benign,drug_response,not_provided,uncertain_significance,pathogenic,uncertain_significance,_other,conflicting_interpretations_of_pathogenicity
pathogenic,likely_pathogenic
pathogenic

说明:单词边界(\y)是零长度断言，它可以放在前面、后面或前后，首先给出单词的开头，第二个以单词结尾，第三个是完整的单词。所以pathogen\y的意思是以pathogen结尾的单词。GNU AWK将单词定义为一个或多个字母、数字或下划线的序列。注意:输出与所需的第4行risk_factor行不同，但是它符合描述，因为该行包含,pathogenic,。

(在gawk 4.2.1中测试)

Answer 3

最好的情况(它还没有完成)，我可以快速进入无需使用word边界正则表达式：

回声"${input….}“\ mawk '$!(NF=NF)~ /非典/‘\ FS='^，*致病[：alpha：]*’OFS=

 1  benign,likely_pathogenic
 2  benign,likely_pathogenic
 3  risk_factor,uncertain_significance,likely_pathogenic,uncertain_significance,_other,benign
 4  risk_factor,uncertain_significance,likely_pathogenic,uncertain_significance,_other,benign
 5  risk_factor,benign,likely_benign,drug_response,not_provided,uncertain_significance,pathogenic,uncertain_significance,_other,
 6  pathogenic,not_provided,benign,likely_pathogenic,likely_benign,risk_factor
 7  benign,likely_pathogenic
 8  benign,likely_pathogenic
 9  ,_other,benign,pathogenic,likely_benign,
10  ,_other,benign,pathogenic,likely_benign,
11  risk_factor,benign,likely_benign,drug_response,not_provided,uncertain_significance,pathogenic,uncertain_significance,_other,
12  pathogenic,likely_pathogenic
13  pathogenic

它可能删除了第9-10行周围太多的内容。