同一行上的多个 grep 输出

Question

这似乎是一个非常琐碎的问题，但我没有足够的使用 grep 和 echo 的经验来自己回答。我看过 here and here 没有成功。

我有一个这样开头的文件（.gff 文件）超过 1,000,000 行。

NW_007577731.1  RefSeq  region  1   3345205 .   +   .   ID=id0;Dbxref=taxon:144197;Name=Unknown;chromosome=Unknown;collection-date=16-Aug-2005;country=USA: Emerald Reef%2C Florida;gbkey=Src;genome=genomic;isolate=25-593;lat-lon=25.6748 N 80.0982 W;mol_type=genomic DNA;sex=male
NW_007577731.1  Gnomon  gene    7982    24854   .   -   .   ID=gene0;Dbxref=GeneID:103352799;Name=LOC103352799;gbkey=Gene;gene=LOC103352799;gene_biotype=protein_coding
NW_007577731.1  Gnomon  mRNA    7982    24854   .   -   .   ID=rna0;Parent=gene0;Dbxref=GeneID:103352799,Genbank:XM_008279367.1;Name=XM_008279367.1;gbkey=mRNA;gene=LOC103352799;model_evidence=Supporting evidence includes similarity to: 22 Proteins%2C and 73%25 coverage of the annotated genomic feature by RNAseq alignments;product=homer protein homolog 3-like;transcript_id=XM_008279367.1
NW_007577731.1  RefSeq  region  1   3345205 .   +   .   ID=id0;Dbxref=taxon:144197;Name=Unknown;chromosome=Unknown;collection-date=16-Aug-2005;country=USA: Emerald Reef%2C Florida;gbkey=Src;genome=genomic;isolate=25-593;lat-lon=25.6748 N 80.0982 W;mol_type=genomic DNA;sex=male
NW_007577731.1  Gnomon  gene    7982    24854   .   -   .   ID=gene0;Dbxref=GeneID:103352799;Name=LOC103352799;gbkey=Gene;gene=LOC103352799;gene_biotype=protein_coding
NW_007577731.1  Gnomon  mRNA    7982    24854   .   -   .   ID=rna0;Parent=gene0;Dbxref=GeneID:103352799,Genbank:XM_008279367.1;Name=XM_008279367.1;gbkey=mRNA;gene=LOC103352799;model_evidence=Supporting evidence includes similarity to: 22 Proteins%2C and 73%25 coverage of the annotated genomic feature by RNAseq alignments;product=homer protein homolog 3-like;transcript_id=XM_008279367.1

我想在第三列中包含 mRNA 的行上进行 grep 以获得此制表符分隔的输出（字段 gene=、product=、transcript_id= 中的值).

LOC103352799    homer protein homolog 3-like    XM_008279367.1
LOC103352799    homer protein homolog 3-like    XM_008279367.1

由于非常缺乏优雅，我可以使用

分别获得 3 列

grep "mRNA\t" myfile.gff|sed s/gene=/@/|cut -f2 -d"@" |cut -f1 -d";"
grep "mRNA\t" myfile.gff|sed s/product=/@/|cut -f2 -d"@" |cut -f1 -d";"
grep "mRNA\t" myfile.gff|sed s/transcript_id=/@/|cut -f2 -d"@" |cut -f1 -d";"

但是如何将这 3 个命令的输出附加到同一行？我试过了

echo -e "`grep "mRNA\t" myfile.gff|sed s/gene=/@/|cut -f2 -d"@" |cut -f1 -d";"`\t`grep "mRNA\t" myfile.gff|sed s/product=/@/|cut -f2 -d"@" |cut -f1 -d";"`\t`grep "mRNA\t" myfile.gff|sed s/transcript_id=/@/|cut -f2 -d"@" |cut -f1 -d";"`"

但这是输出：

LOC103352799
LOC103352799    homer protein homolog 3-like
homer protein homolog 3-like    XM_008279367.1
XM_008279367.1

非常感谢您的帮助！

Answer 1

使用 awk：

$ awk 'BEGIN {
    FS=OFS="\t"                       # field separators to tab
    k="gene,product,transcript_id"    # keyword list
    split(k,a,",")                    # split keywords to a hash for matching
    for(i in a)                       # values to keys
        p[a[i]]
}
=="mRNA" {
    b=""                              # reset buffer b
    split(,a,"[=;]")                # split the data to a hash
    for(i in a)                       # iterate and search
        if(a[i] in p)                 # ... for keywords, if match, 
            b=b (b==""?"":OFS) a[i+1] # ... value is the next, buffer
    print b                           # output buffer
}' file
LOC103352799    homer protein homolog 3-like    XM_008279367.1
LOC103352799    homer protein homolog 3-like    XM_008279367.1

Answer 2

说到单行本，这里是 sed 中的一个：

sed -nE '/\tmRNA\t/ { s/.*gene=([^;]+).*product=([^;]+).*transcript_id=([^;]+)/\t\t/g;p }' file

唯一的假设是 gene、product 和 transcript_id 字段的固定顺序。这可以通过一些改变来解决，但考虑到正则表达式的可读性。

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