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识别模式之间的字符串，如果找到字符串，则打印模式之间的整个区域。最好使用awk

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识别模式之间的字符串，如果找到字符串，则打印模式之间的整个区域。最好使用awk

有类似的问题，但没有一个完全解决我遇到的问题。

简而言之，我需要打印包含我要查找的任何字符串的每个块。每个块起始行包含： <entry version=

欲了解更多详情，请参阅下文：

如果在模式区域（块）内识别出某个字符串，我想搜索打印模式之间的每个整个区域（块）的大型文件（数十万行）。

我知道我可以打印模式之间的整个区域，其中这些块的开始和结束标识符是“/<entry version=”，使用： awk '/<entry version=/{flag=1} flag; /<entry version=/{flag=0}'

但是如果在这些模式之间找到某些字符串，如何让它只打印整个块？

对于块区域来说，真实数据的最短部分看起来像这样（尽管实际上每个块都有数千行长），我要感谢 Terdon 整理了一个更好的示例供我使用：

<entry version="21.1" url="http://v21.proteinatlas.org/ENSG00000000003">   
        <name>TSPAN6</name>                                                                                                                             
        <synonym>T245</synonym>
        <synonym>TM4SF6</synonym>
        <synonym>TSPAN-6</synonym>
        <identifier id="ENSG00000000003" db="Ensembl" version="103.38" assembly="GRCh38.p13" gencodeVersion="37">
                <xref id="O43657" db="Uniprot/SWISSPROT"/> 
                <xref id="7105" db="NCBI GeneID"/>
        </identifier>  
        <proteinClasses>   
                <proteinClass source="MDM" id="Ma" parent_id="" name="Predicted membrane proteins"/>

在上面的真实格式中，我将检查特定字符串的名称和同义词，因此如果我正在寻找“TSPAN6”，那么将打印该块。每个块都有数千行，因此下面只是一个虚构的迷你版本，用于解释我如何根据块内的字符串匹配来打印块。

这是一个示例，如果我的字符串是“MEMSAT”和“TNMD”
示例输入：

 <entry version="21.1" url="http://v21.proteinatlas.org/ENSG00000000003">
        <name>TSPAN6</name>
        <synonym>T245</synonym>
        <synonym>TM4SF6</synonym>
        <synonym>TSPAN-6</synonym>
        <identifier id="ENSG00000000003" db="Ensembl" version="103.38" assembly="GRCh38.p13" gencodeVersion="37">
            <xref id="O43657" db="Uniprot/SWISSPROT"/>
            <xref id="7105" db="NCBI GeneID"/>
        </identifier>
        <proteinClasses>
            <proteinClass source="MDM" id="Ma" parent_id="" name="Predicted membrane proteins"/>
            <proteinClass source="Ezkurdia et al 2014" id="Eb" parent_id="" name="Protein evidence (Ezkurdia et al 2014)"/>
        </proteinClasses>
        <proteinEvidence evidence="Evidence at protein level">
            <evidence source="HPA" evidence="Evidence at transcript level"/>
            <evidence source="MS" evidence="Not available"/>
            <evidence source="UniProt" evidence="Evidence at protein level"/>
        </proteinEvidence>
  </entry>
    <entry version="21.1" url="http://v21.proteinatlas.org/ENSG00000000005">
        <name>TNMD</name>
        <synonym>BRICD4</synonym>
        <synonym>ChM1L</synonym>
        <synonym>myodulin</synonym>
        <synonym>TEM</synonym>
        <synonym>tendin</synonym>
        <identifier id="ENSG00000000005" db="Ensembl" version="103.38" assembly="GRCh38.p13" gencodeVersion="37">
            <xref id="Q9H2S6" db="Uniprot/SWISSPROT"/>
            <xref id="64102" db="NCBI GeneID"/>
        </identifier>
        <proteinClasses>
            <proteinClass source="MDM" id="Ma" parent_id="" name="Predicted membrane proteins"/>
            <proteinClass source="MDM" id="Md" parent_id="" name="Membrane proteins predicted by MDM"/>
            <proteinClass source="MEMSAT3" id="Me" parent_id="" name="MEMSAT3 predicted membrane proteins"/>
        </proteinClasses>
        <proteinEvidence evidence="Evidence at protein level">
            <evidence source="HPA" evidence="Evidence at transcript level"/>
            <evidence source="MS" evidence="Not available"/>
            <evidence source="UniProt" evidence="Evidence at protein level"/>
        </proteinEvidence>
  </entry>

输出示例：

    <entry version="21.1" url="http://v21.proteinatlas.org/ENSG00000000005">
        <name>TNMD</name>
        <synonym>BRICD4</synonym>
        <synonym>ChM1L</synonym>
        <synonym>myodulin</synonym>
        <synonym>TEM</synonym>
        <synonym>tendin</synonym>
        <identifier id="ENSG00000000005" db="Ensembl" version="103.38" assembly="GRCh38.p13" gencodeVersion="37">
            <xref id="Q9H2S6" db="Uniprot/SWISSPROT"/>
            <xref id="64102" db="NCBI GeneID"/>
        </identifier>
        <proteinClasses>
            <proteinClass source="MDM" id="Ma" parent_id="" name="Predicted membrane proteins"/>
            <proteinClass source="MDM" id="Md" parent_id="" name="Membrane proteins predicted by MDM"/>
            <proteinClass source="MEMSAT3" id="Me" parent_id="" name="MEMSAT3 predicted membrane proteins"/>
        </proteinClasses>
        <proteinEvidence evidence="Evidence at protein level">
            <evidence source="HPA" evidence="Evidence at transcript level"/>
            <evidence source="MS" evidence="Not available"/>
            <evidence source="UniProt" evidence="Evidence at protein level"/>
        </proteinEvidence>
  </entry>

答案1

使用乐（以前称为 Perl_6）

~$ raku -MXML -e 'my $xml = open-xml($*ARGFILES.Str);  \
                  .say for $xml.getElementsByTagName("entry").grep(/ TSPAN6 | TNMD /).pairs;'  file.xml

#OR

~$ raku -MXML -e 'my @xml = open-xml($*ARGFILES.Str).getElementsByTagName("entry");  \
                  my @names = <TSPAN6 TNMD>; .say for @xml.grep(/@names/).pairs;' file.xml

如果您拥有真实的 XML 文件，那么最好使用真实的 XML 解析器。在上面的代码中，您使用XML命令行标志调用 Raku 社区模块-MXML（顺便说一句，这与使用 Perl 在命令行调用模块的方式相同）。花点时间熟悉当前的 XML 模式，然后相应地规划您的编码：

https://www. Proteinatlas.org/download/ Proteinatlas.xsd

上面的第一个答案将您的文件打开为$xmlXML 文档。然后 XML 文档被分解为entry使用命名的（顶级）元素.getElementsByTagName();。最后，遍历每个元素grep以获得包含所需字符串的元素。

上面的第二个答案搜索名为的 XML 元素entry并将文件打开到@xmlRaku 数组中。然后遍历每个元素grep以获得包含所需字符串的元素，这些字符串已保存在数组中@names。

示例输入（取自@terdon的优秀答案）：

<?xml version="1.0" encoding="UTF-8"?>
<proteinAtlas xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://v21.proteinatlas.org/download/proteinatlas.xsd" schemaVersion="2.6">
    <entry version="21.1" url="http://v21.proteinatlas.org/ENSG00000000003">
        <name>TSPAN6</name>
        <synonym>T245</synonym>
        <synonym>TM4SF6</synonym>
        <synonym>TSPAN-6</synonym>
        <identifier id="ENSG00000000003" db="Ensembl" version="103.38" assembly="GRCh38.p13" gencodeVersion="37">
            <xref id="O43657" db="Uniprot/SWISSPROT"/>
            <xref id="7105" db="NCBI GeneID"/>
        </identifier>
        <proteinClasses>
            <proteinClass source="MDM" id="Ma" parent_id="" name="Predicted membrane proteins"/>
            <proteinClass source="Ezkurdia et al 2014" id="Eb" parent_id="" name="Protein evidence (Ezkurdia et al 2014)"/>
        </proteinClasses>
        <proteinEvidence evidence="Evidence at protein level">
            <evidence source="HPA" evidence="Evidence at transcript level"/>
            <evidence source="MS" evidence="Not available"/>
            <evidence source="UniProt" evidence="Evidence at protein level"/>
        </proteinEvidence>
  </entry>
    <entry version="21.1" url="http://v21.proteinatlas.org/ENSG00000000005">
        <name>TNMD</name>
        <synonym>BRICD4</synonym>
        <synonym>ChM1L</synonym>
        <synonym>myodulin</synonym>
        <synonym>TEM</synonym>
        <synonym>tendin</synonym>
        <identifier id="ENSG00000000005" db="Ensembl" version="103.38" assembly="GRCh38.p13" gencodeVersion="37">
            <xref id="Q9H2S6" db="Uniprot/SWISSPROT"/>
            <xref id="64102" db="NCBI GeneID"/>
        </identifier>
        <proteinClasses>
            <proteinClass source="MDM" id="Ma" parent_id="" name="Predicted membrane proteins"/>
            <proteinClass source="MDM" id="Md" parent_id="" name="Membrane proteins predicted by MDM"/>
            <proteinClass source="MEMSAT3" id="Me" parent_id="" name="MEMSAT3 predicted membrane proteins"/>
        </proteinClasses>
        <proteinEvidence evidence="Evidence at protein level">
            <evidence source="HPA" evidence="Evidence at transcript level"/>
            <evidence source="MS" evidence="Not available"/>
            <evidence source="UniProt" evidence="Evidence at protein level"/>
        </proteinEvidence>
  </entry>
</proteinAtlas>

示例输出：

0 => <entry version="21.1" url="http://v21.proteinatlas.org/ENSG00000000003">
        <name>TSPAN6</name>
        <synonym>T245</synonym>
        <synonym>TM4SF6</synonym>
        <synonym>TSPAN-6</synonym>
        <identifier version="103.38" gencodeVersion="37" assembly="GRCh38.p13" db="Ensembl" id="ENSG00000000003">
            <xref id="O43657" db="Uniprot/SWISSPROT"/>
            <xref db="NCBI GeneID" id="7105"/>
        </identifier>
        <proteinClasses>
            <proteinClass id="Ma" source="MDM" parent_id="" name="Predicted membrane proteins"/>
            <proteinClass name="Protein evidence (Ezkurdia et al 2014)" parent_id="" id="Eb" source="Ezkurdia et al 2014"/>
        </proteinClasses>
        <proteinEvidence evidence="Evidence at protein level">
            <evidence source="HPA" evidence="Evidence at transcript level"/>
            <evidence evidence="Not available" source="MS"/>
            <evidence evidence="Evidence at protein level" source="UniProt"/>
        </proteinEvidence>
  </entry>
1 => <entry version="21.1" url="http://v21.proteinatlas.org/ENSG00000000005">
        <name>TNMD</name>
        <synonym>BRICD4</synonym>
        <synonym>ChM1L</synonym>
        <synonym>myodulin</synonym>
        <synonym>TEM</synonym>
        <synonym>tendin</synonym>
        <identifier version="103.38" assembly="GRCh38.p13" db="Ensembl" gencodeVersion="37" id="ENSG00000000005">
            <xref id="Q9H2S6" db="Uniprot/SWISSPROT"/>
            <xref db="NCBI GeneID" id="64102"/>
        </identifier>
        <proteinClasses>
            <proteinClass name="Predicted membrane proteins" source="MDM" id="Ma" parent_id=""/>
            <proteinClass parent_id="" id="Md" name="Membrane proteins predicted by MDM" source="MDM"/>
            <proteinClass id="Me" name="MEMSAT3 predicted membrane proteins" parent_id="" source="MEMSAT3"/>
        </proteinClasses>
        <proteinEvidence evidence="Evidence at protein level">
            <evidence evidence="Evidence at transcript level" source="HPA"/>
            <evidence evidence="Not available" source="MS"/>
            <evidence evidence="Evidence at protein level" source="UniProt"/>
        </proteinEvidence>
  </entry>

上面的调用pairs只是对输出元素进行编号。最后，@terdon 的评论正确地指出，grep基因名称可能不是您最安全的选择。如果您改为搜索Ids，则可以极大地简化返回值（如果确实如此，返回的有限子集对您有用）：

~$ raku -MXML -e 'my $xml=open-xml($*ARGFILES.Str); put $xml.getElementById("ENSG00000000003"|"ENSG00000000005").pairs;' file.xml

返回：

0   <identifier version="103.38" gencodeVersion="37" id="ENSG00000000003" db="Ensembl" assembly="GRCh38.p13">
            <xref id="O43657" db="Uniprot/SWISSPROT"/>
            <xref id="7105" db="NCBI GeneID"/>
        </identifier>
0   <identifier gencodeVersion="37" assembly="GRCh38.p13" version="103.38" db="Ensembl" id="ENSG00000000005">
            <xref db="Uniprot/SWISSPROT" id="Q9H2S6"/>
            <xref db="NCBI GeneID" id="64102"/>
        </identifier>

https://github.com/raku-community-modules/XML
https://rakudo.org/
https://raku.org

答案2

假设输入是格式良好的 XML 文档（如特登的回答，但不是问题中显示的内容），您可以用来输出具有特定和属性的xmlstarlet每个节点的副本。entrynameproteinClasssource

xmlstarlet select --template \
   --copy-of '//entry[name = "TNMD" and proteinClasses/proteinClass/@source = "MEMSAT3"]' \
   -nl file

这将选择entry具有特定属性值的所有节点name，并且该节点还具有具有proteinClasses/proteinClass特定属性值的子节点source。entry将输出每个匹配节点的副本，并添加尾随换行符。

答案3

您可以在 GNU awk 中通过使用</entry[^>]*>作为记录分隔符来执行此操作。例如，使用此文件作为输入：

<?xml version="1.0" encoding="UTF-8"?>
<proteinAtlas xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://v21.proteinatlas.org/download/proteinatlas.xsd" schemaVersion="2.6">
    <entry version="21.1" url="http://v21.proteinatlas.org/ENSG00000000003">
        <name>TSPAN6</name>
        <synonym>T245</synonym>
        <synonym>TM4SF6</synonym>
        <synonym>TSPAN-6</synonym>
        <identifier id="ENSG00000000003" db="Ensembl" version="103.38" assembly="GRCh38.p13" gencodeVersion="37">
            <xref id="O43657" db="Uniprot/SWISSPROT"/>
            <xref id="7105" db="NCBI GeneID"/>
        </identifier>
        <proteinClasses>
            <proteinClass source="MDM" id="Ma" parent_id="" name="Predicted membrane proteins"/>
            <proteinClass source="Ezkurdia et al 2014" id="Eb" parent_id="" name="Protein evidence (Ezkurdia et al 2014)"/>
        </proteinClasses>
        <proteinEvidence evidence="Evidence at protein level">
            <evidence source="HPA" evidence="Evidence at transcript level"/>
            <evidence source="MS" evidence="Not available"/>
            <evidence source="UniProt" evidence="Evidence at protein level"/>
        </proteinEvidence>
  </entry>
    <entry version="21.1" url="http://v21.proteinatlas.org/ENSG00000000005">
        <name>TNMD</name>
        <synonym>BRICD4</synonym>
        <synonym>ChM1L</synonym>
        <synonym>myodulin</synonym>
        <synonym>TEM</synonym>
        <synonym>tendin</synonym>
        <identifier id="ENSG00000000005" db="Ensembl" version="103.38" assembly="GRCh38.p13" gencodeVersion="37">
            <xref id="Q9H2S6" db="Uniprot/SWISSPROT"/>
            <xref id="64102" db="NCBI GeneID"/>
        </identifier>
        <proteinClasses>
            <proteinClass source="MDM" id="Ma" parent_id="" name="Predicted membrane proteins"/>
            <proteinClass source="MDM" id="Md" parent_id="" name="Membrane proteins predicted by MDM"/>
            <proteinClass source="MEMSAT3" id="Me" parent_id="" name="MEMSAT3 predicted membrane proteins"/>
        </proteinClasses>
        <proteinEvidence evidence="Evidence at protein level">
            <evidence source="HPA" evidence="Evidence at transcript level"/>
            <evidence source="MS" evidence="Not available"/>
            <evidence source="UniProt" evidence="Evidence at protein level"/>
        </proteinEvidence>
  </entry>
</proteinAtlas>

您可以通过以下方式获取数据TNMD：

$ gawk 'BEGIN{ RS="</entry[^>]*>" } /TNMD/' a

    <entry version="21.1" url="http://v21.proteinatlas.org/ENSG00000000005">
        <name>TNMD</name>
        <synonym>BRICD4</synonym>
        <synonym>ChM1L</synonym>
        <synonym>myodulin</synonym>
        <synonym>TEM</synonym>
        <synonym>tendin</synonym>
        <identifier id="ENSG00000000005" db="Ensembl" version="103.38" assembly="GRCh38.p13" gencodeVersion="37">
            <xref id="Q9H2S6" db="Uniprot/SWISSPROT"/>
            <xref id="64102" db="NCBI GeneID"/>
        </identifier>
        <proteinClasses>
            <proteinClass source="MDM" id="Ma" parent_id="" name="Predicted membrane proteins"/>
            <proteinClass source="MDM" id="Md" parent_id="" name="Membrane proteins predicted by MDM"/>
            <proteinClass source="MEMSAT3" id="Me" parent_id="" name="MEMSAT3 predicted membrane proteins"/>
        </proteinClasses>
        <proteinEvidence evidence="Evidence at protein level">
            <evidence source="HPA" evidence="Evidence at transcript level"/>
            <evidence source="MS" evidence="Not available"/>
            <evidence source="UniProt" evidence="Evidence at protein level"/>
        </proteinEvidence>

这只是意味着“如果匹配则打印此行TNMD”。当然，如果该行是类似的东西，它也会打印，87% identity to TNMD并且它肯定会在各种边缘情况下中断，因为我们没有使用正确的解析器。

使用适当的解析器，您可以准确指定字符串应该在的位置。

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