Question

这个问题有点令人困惑，所以我只想展示一个例子。

假设我有以下情况：

$ grep -P "locus_tag\tM715_1000193188" Genome.tbl -B1 -A8
193188  193066  gene
            locus_tag   M715_1000193188
193188  193066  mRNA
            product hypothetical protein
            protein_id  gnl|CorradiLab|M715_1000193188
            transcript_id   gnl|CorradiLab|M715_mrna1000193188
193188  193066  CDS
        product hypothetical protein
        protein_id  gnl|CorradiLab|M715_1000193188
        transcript_id   gnl|CorradiLab|M715_mrna1000193188

我想在“locus_tag M715_1000193188”之后的8行添加“＃”，以便我的修改后的文件如下所示：

193188  193066  gene
            locus_tag   M715_1000193188
#193188 193066  mRNA
#           product hypothetical protein
#           protein_id  gnl|CorradiLab|M715_1000193188
#           transcript_id   gnl|CorradiLab|M715_mrna1000193188
#193188 193066  CDS
#       product hypothetical protein
#       protein_id  gnl|CorradiLab|M715_1000193188
#       transcript_id   gnl|CorradiLab|M715_mrna1000193188

基本上我有一个包含~3000个不同基因座标签的文件，其中300个我需要注释掉mRNA和CDS功能，所以跟随locus_tag行的8行。

用sed做任何可行的方法吗？文件中还有其他类型的信息需要保持不变。

谢谢，阿德里安

Answer 1

如果您可以使用awk，则应执行以下操作：

awk 'f&&f-- {$0="#"$0} /locus_tag/ {f=8} 1' file
193188  193066  gene
            locus_tag   M715_1000193188
#193188  193066  mRNA
#            product hypothetical protein
#            protein_id  gnl|CorradiLab|M715_1000193188
#            transcript_id   gnl|CorradiLab|M715_mrna1000193188
#193188  193066  CDS
#        product hypothetical protein
#        protein_id  gnl|CorradiLab|M715_1000193188
#        transcript_id   gnl|CorradiLab|M715_mrna1000193188

Answer 2

sed支持范围Addresses，可以在此处执行您想要的操作。

sed -e '/locus_tag\tM715_1000193188/,+8s/^/#/' file

如评论中所述，此范围地址格式是GNU特定的。

Answer 3

$ cat tst.awk
BEGIN { split(tags,tmp); for (i in tmp) tagsA[tmp[i]] }
c&&c-- { $0 = "#" $0 }
($(NF-1) == "locus_tag") && ($NF in tagsA) { c=8 }
{ print }

$ awk -v tags="M715_1000193188 M715_1000193189 M715_1000193190" -f tst.awk file
193188  193066  gene
            locus_tag   M715_1000193188
#193188  193066  mRNA
#            product hypothetical protein
#            protein_id  gnl|CorradiLab|M715_1000193188
#            transcript_id   gnl|CorradiLab|M715_mrna1000193188
#193188  193066  CDS
#        product hypothetical protein
#        protein_id  gnl|CorradiLab|M715_1000193188
#        transcript_id   gnl|CorradiLab|M715_mrna1000193188

只需列出您关注的所有300个基因座标签值，如上所示为3个示例。

Answer 4

这可能适合你（GNU sed）：

sed 's/.*/\\#locus_tag\\s*&#,+9{\\#locus_tag\\s*&#n;s|^|#|}/' tag_file |
sed -i -f - file

这会从标记文件创建一个sed脚本，并在标记匹配后的八行前面添加#。

在匹配STRING的前8行前面添加“＃”

4 个答案: