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删除括号内以外的所有内容

tag-icon • tag-icon text-formatting bioinformatics
删除括号内以外的所有内容

我想删除不在括号内的所有内容，包括括号，仅在以“>”开头的行中。有 sed 替代品吗？另外，想按字母顺序对行进行排序，即以“>”开头的行及其下一行。

输入示例：

>ID:000:FLKLNFIA_00192 |[Ignicoccus_hospitalis_KIN4-I.gbfspecies]|strain|Ignicoccus_hospitalis_KIN4-I.gbf|LSU ribosomal protei..|447|FLKLNFIA_1(1297538):162644-163090:1 ^^ Archaeagenomesparanahui Ignicoccus_hospitalis_KIN4-I.gbfspecies strain strain.|neighbours:ID:000:FLKLNFIA_00191(1),ID:000:FLKLNFIA_00193(1)|neighbour_genes:LSU ribosomal protei..,SSU ribosomal protei..| 
ATGAGTGTGACTA---TTT---GCAATCAGCTAGCTACTACGTACTGATCGTAGCTGACG
>ID:000:MGCDKLCO_01184 |[Archaeoglobus_fulgidus_DSM_4304.gbfspecies]|strain|Archaeoglobus_fulgidus_DSM_4304.gbf|50S ribosomal protei..|471|MGCDKLCO_1(2178400):1005279-1005749:1 ^^ Archaeagenomesparanahui Archaeoglobus_fulgidus_DSM_4304.gbfspecies strain strain.|neighbours:ID:000:MGCDKLCO_01183(1),ID:000:MGCDKLCO_01185(1)|neighbour_genes:LSU ribosomal protei..,SSU ribosomal protei..|
ATGCGCGCGATAGCTAGCTAGCTAGCTTTAGGGGGATTAGCTA----ACTCTGATTCGGA

预期输出：

>Archaeoglobus_fulgidus_DSM_4304.gbfspecies
ATGCGCGCGATAGCTAGCTAGCTAGCTTTAGGGGGATTAGCTA----ACTCTGATTCGGA
>Ignicoccus_hospitalis_KIN4-I.gbfspecies
ATGAGTGTGACTA---TTT---GCAATCAGCTAGCTACTACGTACTGATCGTAGCTGACG

谢谢

答案1

和perl：

perl -ne 'push @l, ">" . join("", /\[(.*?)\]/g) . "\n" . <>;
          END{print for sort @l}' your-file

和sed：

<your-file sed 's/^[^[]*\[/>/
                s/\][^[]*\[\{0,1\}//g
                N;s/\n/\[/' |
  sort |
  tr '[' '\n'

答案2

我的（复杂的）建议：

cat file | grep -Po "^[CGTA-]*$|^>.*$" | grep -Po "(?<=\[).*(?=])|^[ACGT-]*$" | awk '{printf (NR%2==0) ? $0 "\n" : ">"$0"::"}' | sort | sed 's/#/\n/'

Grep 仅包含包含字符的行CGTA- 以及以以下字符开头的行>

grep -Po "^[CGTA-]*$|^>.*$"

仅 Grep 括号内的内容（排除它们）以及与模式匹配的行ACGT-

| grep -Po "(?<=\[).*(?=])|^[ACGT-]*$"

连接每两行，添加分隔符#和首字母>，然后排序

| awk '{printf (NR%2==0) ? $0 "\n" : ">"$0"#"}' | sort

#最后用新行替换分隔符

| sed 's/#/\n/'

输出：

>Archaeoglobus_fulgidus_DSM_4304.gbfspecies
ATGCGCGCGATAGCTAGCTAGCTAGCTTTAGGGGGATTAGCTA----ACTCTGATTCGGA
>Ignicoccus_hospitalis_KIN4-I.gbfspecies
ATGAGTGTGACTA---TTT---GCAATCAGCTAGCTACTACGTACTGATCGTAGCTGACG

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