在匹配条件的标题下方打印行

Question

我有一个这样的数据库：

>2654570298
MRNYSYKGKWEKLLTPEIVKKLTLINEFKGEQRLFIKAHKDELKELSELA
KIQSTEASNKIEGIFTSDDRFKSLAQAKTTPRNRNESEIAGYRDVLNTIH
DSYEYIPISASYFLQLHRDLYKFVAKNDVGKFKSSDNIIRETDEKGNERL
RFRPVPAWETPAAIDELCKAYADAKEEIDPLILNAMFILDFLCIHPFNDG
NGRMSRLLTLLLLYKTGFIVGKYISIEKIIEESKETYYEVLQDSLVGWHE
NENDYKPFVNYMLGVIVNAYKEFESRTELVTNPNLTKSDRIREIIKDHIG
TITKAELLEMNPDISDTTVQRTLAKLLKNNDIKKIGGGRYTKYTWNTEEQ

>2654570299|K03427
MITGELKNKIDGLWDVFAAGGLVNPLEVIEQITYLMFIKDLDDVDKRKEK
ESAMLGLPYKSIFAGEVKIGDRTIEGTQLKWSVFHDFSAGRMYAIMQEWV
FPFIKNLHSDKNSTYSKYMDDAIFKFPTPLLLSKVVDSLDEIYEIMNSTL
VLDVRGDVYEYLLNKIASAGRNGQFRTPRHIIRMMVEMVEPKADDVICDP
GDLLKVCKTKKTELLFLALFLRMLKVGGRCACIVPDGVLFGSSKAHKDIR
KQVVEENRLEAVISMPSGVFKPYAGVSTAILIFTKTGHGGTDNVWFYDMT
ADGYSLDDKRTPVSENDIPDIIERFKNLDKEIDRERTDKSFMVPKQDIAD
NDYDLSINKYKEVVYEKIEYPPTSEIMADIREIEMEIGKEMDELEKLLNI

>2654570301
MNESELYKELGILTKDKSKWAENIQYVSSLLNHESAKIQAKALWLLGEMG
LEYPDSIQDAVPMVASFCDSENALLRERAVNALGRIGRGNYNLIEPYWSD
LFRFASDDEPKVRLSFIWASENVATNTPDIYENHMSVFESLLHDIDDKVR
MESPEIFRVLGKRRPEFVIPYIEQLQKMAETDSNRVVRIHSLGAIKVTTS
K

>2654570302
MWNMIWPLVLIVGSNCFYNICTKSMPEGTNTFGALTVTYLVGAVLSAVLF
VVSVKPAGVLNEISKINWTSFVLGLVIVGLEAGYVFLYRAGWKVSNGALT
ANICLAIALIVIGFLLYKESISIKQVAGIVVCGFGLFLING

>2654570303|K01153
MKNKELLKRVGYVVLICLSFFVATWYFFENNKICTICWIAIGSKNVYDLV
HRIKNSKKED

我想过滤它，只打印标题包含“|K”的序列，使用 awk、grep 或类似的东西。期望的输出：

>2654570299|K03427
MITGELKNKIDGLWDVFAAGGLVNPLEVIEQITYLMFIKDLDDVDKRKEK
ESAMLGLPYKSIFAGEVKIGDRTIEGTQLKWSVFHDFSAGRMYAIMQEWV
FPFIKNLHSDKNSTYSKYMDDAIFKFPTPLLLSKVVDSLDEIYEIMNSTL
VLDVRGDVYEYLLNKIASAGRNGQFRTPRHIIRMMVEMVEPKADDVICDP
GDLLKVCKTKKTELLFLALFLRMLKVGGRCACIVPDGVLFGSSKAHKDIR
KQVVEENRLEAVISMPSGVFKPYAGVSTAILIFTKTGHGGTDNVWFYDMT
ADGYSLDDKRTPVSENDIPDIIERFKNLDKEIDRERTDKSFMVPKQDIAD
NDYDLSINKYKEVVYEKIEYPPTSEIMADIREIEMEIGKEMDELEKLLNI

>2654570303|K01153
MKNKELLKRVGYVVLICLSFFVATWYFFENNKICTICWIAIGSKNVYDLV
HRIKNSKKED

请注意，一个标题和下一个标题之间的行数并不总是相同的，换行符总是将一个序列和后面的标题分开。

有人可以帮忙吗？

Answer 1

同样使用awk这可以帮助你：

awk '/^>/ {f=/\|K/} f' file
>2654570299|K03427
MITGELKNKIDGLWDVFAAGGLVNPLEVIEQITYLMFIKDLDDVDKRKEK
ESAMLGLPYKSIFAGEVKIGDRTIEGTQLKWSVFHDFSAGRMYAIMQEWV
FPFIKNLHSDKNSTYSKYMDDAIFKFPTPLLLSKVVDSLDEIYEIMNSTL
VLDVRGDVYEYLLNKIASAGRNGQFRTPRHIIRMMVEMVEPKADDVICDP
GDLLKVCKTKKTELLFLALFLRMLKVGGRCACIVPDGVLFGSSKAHKDIR
KQVVEENRLEAVISMPSGVFKPYAGVSTAILIFTKTGHGGTDNVWFYDMT
ADGYSLDDKRTPVSENDIPDIIERFKNLDKEIDRERTDKSFMVPKQDIAD
NDYDLSINKYKEVVYEKIEYPPTSEIMADIREIEMEIGKEMDELEKLLNI

>2654570303|K01153
MKNKELLKRVGYVVLICLSFFVATWYFFENNKICTICWIAIGSKNVYDLV
HRIKNSKKED

• 如果f 为真，则打印这些行。默认情况下，在awk 中，当条件评估为真时，会打印 $0 的内容。
• 您可以通过print 看到f 的值。
• 以及哪些行或记录是真实的：

awk '/^>/ {f=/\|K/} f {print NR, f}' file

Answer 2

使用 awk 或 sed：

sed -e '/|K/, /^$/ p; d' database.txt
awk '/\|K/, /^$/' database.txt

它们都做完全相同的事情——它们检查一行上的|K 并打印，直到他们看到下一个空白行。在 sed 语法中，打印是显式的 p（后面的 d 清除缓冲区以移动到下一个输入行），而 awk 示例利用了更隐式的 awk“默认操作”行为。

这两个工具在匹配语法中使用的正则表达式语言版本有一点区别——因为`|`字符可以有特殊的含义，所以必须在awk示例中进行转义.

为了更深入地理解语法，awk 和 sed 都记录在它们的“手册页”中——请参阅此文档以了解有关语言如何工作的更多信息。

Answer 3

如果您取消设置记录分隔符 (RS)，awk 会将每个部分视为 一个记录，例如查找其中包含|K 的记录：

awk '/\|K/' RS=

输出：

>2654570299|K03427
MITGELKNKIDGLWDVFAAGGLVNPLEVIEQITYLMFIKDLDDVDKRKEK
ESAMLGLPYKSIFAGEVKIGDRTIEGTQLKWSVFHDFSAGRMYAIMQEWV
FPFIKNLHSDKNSTYSKYMDDAIFKFPTPLLLSKVVDSLDEIYEIMNSTL
VLDVRGDVYEYLLNKIASAGRNGQFRTPRHIIRMMVEMVEPKADDVICDP
GDLLKVCKTKKTELLFLALFLRMLKVGGRCACIVPDGVLFGSSKAHKDIR
KQVVEENRLEAVISMPSGVFKPYAGVSTAILIFTKTGHGGTDNVWFYDMT
ADGYSLDDKRTPVSENDIPDIIERFKNLDKEIDRERTDKSFMVPKQDIAD
NDYDLSINKYKEVVYEKIEYPPTSEIMADIREIEMEIGKEMDELEKLLNI
>2654570303|K01153
MKNKELLKRVGYVVLICLSFFVATWYFFENNKICTICWIAIGSKNVYDLV
HRIKNSKKED

现在，如果您希望输出是双换行符并且只匹配标题，您可以更改字段分隔符（FS）和输出记录分隔符（ORS），例如：

awk '$1 ~ /\|K/' RS= FS='\n' ORS='\n\n'

输出：

>2654570299|K03427
MITGELKNKIDGLWDVFAAGGLVNPLEVIEQITYLMFIKDLDDVDKRKEK
ESAMLGLPYKSIFAGEVKIGDRTIEGTQLKWSVFHDFSAGRMYAIMQEWV
FPFIKNLHSDKNSTYSKYMDDAIFKFPTPLLLSKVVDSLDEIYEIMNSTL
VLDVRGDVYEYLLNKIASAGRNGQFRTPRHIIRMMVEMVEPKADDVICDP
GDLLKVCKTKKTELLFLALFLRMLKVGGRCACIVPDGVLFGSSKAHKDIR
KQVVEENRLEAVISMPSGVFKPYAGVSTAILIFTKTGHGGTDNVWFYDMT
ADGYSLDDKRTPVSENDIPDIIERFKNLDKEIDRERTDKSFMVPKQDIAD
NDYDLSINKYKEVVYEKIEYPPTSEIMADIREIEMEIGKEMDELEKLLNI

>2654570303|K01153
MKNKELLKRVGYVVLICLSFFVATWYFFENNKICTICWIAIGSKNVYDLV
HRIKNSKKED

Answer 4

我会使用 GNU AWK 来完成这个任务，让 file.txt 内容成为

>2654570298
MRNYSYKGKWEKLLTPEIVKKLTLINEFKGEQRLFIKAHKDELKELSELA
KIQSTEASNKIEGIFTSDDRFKSLAQAKTTPRNRNESEIAGYRDVLNTIH
DSYEYIPISASYFLQLHRDLYKFVAKNDVGKFKSSDNIIRETDEKGNERL
RFRPVPAWETPAAIDELCKAYADAKEEIDPLILNAMFILDFLCIHPFNDG
NGRMSRLLTLLLLYKTGFIVGKYISIEKIIEESKETYYEVLQDSLVGWHE
NENDYKPFVNYMLGVIVNAYKEFESRTELVTNPNLTKSDRIREIIKDHIG
TITKAELLEMNPDISDTTVQRTLAKLLKNNDIKKIGGGRYTKYTWNTEEQ

>2654570299|K03427
MITGELKNKIDGLWDVFAAGGLVNPLEVIEQITYLMFIKDLDDVDKRKEK
ESAMLGLPYKSIFAGEVKIGDRTIEGTQLKWSVFHDFSAGRMYAIMQEWV
FPFIKNLHSDKNSTYSKYMDDAIFKFPTPLLLSKVVDSLDEIYEIMNSTL
VLDVRGDVYEYLLNKIASAGRNGQFRTPRHIIRMMVEMVEPKADDVICDP
GDLLKVCKTKKTELLFLALFLRMLKVGGRCACIVPDGVLFGSSKAHKDIR
KQVVEENRLEAVISMPSGVFKPYAGVSTAILIFTKTGHGGTDNVWFYDMT
ADGYSLDDKRTPVSENDIPDIIERFKNLDKEIDRERTDKSFMVPKQDIAD
NDYDLSINKYKEVVYEKIEYPPTSEIMADIREIEMEIGKEMDELEKLLNI

>2654570301
MNESELYKELGILTKDKSKWAENIQYVSSLLNHESAKIQAKALWLLGEMG
LEYPDSIQDAVPMVASFCDSENALLRERAVNALGRIGRGNYNLIEPYWSD
LFRFASDDEPKVRLSFIWASENVATNTPDIYENHMSVFESLLHDIDDKVR
MESPEIFRVLGKRRPEFVIPYIEQLQKMAETDSNRVVRIHSLGAIKVTTS
K

>2654570302
MWNMIWPLVLIVGSNCFYNICTKSMPEGTNTFGALTVTYLVGAVLSAVLF
VVSVKPAGVLNEISKINWTSFVLGLVIVGLEAGYVFLYRAGWKVSNGALT
ANICLAIALIVIGFLLYKESISIKQVAGIVVCGFGLFLING

>2654570303|K01153
MKNKELLKRVGYVVLICLSFFVATWYFFENNKICTICWIAIGSKNVYDLV
HRIKNSKKED

然后

awk 'BEGIN{RS=ORS="\n\n"}index($0,"|K"){print}' file.txt

输出

>2654570299|K03427
MITGELKNKIDGLWDVFAAGGLVNPLEVIEQITYLMFIKDLDDVDKRKEK
ESAMLGLPYKSIFAGEVKIGDRTIEGTQLKWSVFHDFSAGRMYAIMQEWV
FPFIKNLHSDKNSTYSKYMDDAIFKFPTPLLLSKVVDSLDEIYEIMNSTL
VLDVRGDVYEYLLNKIASAGRNGQFRTPRHIIRMMVEMVEPKADDVICDP
GDLLKVCKTKKTELLFLALFLRMLKVGGRCACIVPDGVLFGSSKAHKDIR
KQVVEENRLEAVISMPSGVFKPYAGVSTAILIFTKTGHGGTDNVWFYDMT
ADGYSLDDKRTPVSENDIPDIIERFKNLDKEIDRERTDKSFMVPKQDIAD
NDYDLSINKYKEVVYEKIEYPPTSEIMADIREIEMEIGKEMDELEKLLNI

>2654570303|K01153
MKNKELLKRVGYVVLICLSFFVATWYFFENNKICTICWIAIGSKNVYDLV
HRIKNSKKED

说明：我将行分隔符和输出行分隔符设置为双换行符，即空白行，因此每个部分都被视为单行。然后我使用index 函数来检查部分是否包含|K。如果没有匹配，此函数返回 0，如果找到匹配的位置。 print 仅在后一种情况下完成。请注意，此函数接受字符串 ("|K") 而不是模式 (/\|K/)，因此我不必关心像 | 这样具有特殊含义的字符。如果您想了解更多关于RS、ORS 或其他内置AWK 变量的信息，请阅读8 Powerful Awk Built-in Variables – FS, OFS, RS, ORS, NR, NF, FILENAME, FNR

（在 gawk 4.2.1 中测试）