如何通过给定两个文件在特定的单词之间提取行？

Question

我有两个文件1和2。文件1包含从C和D开始的代谢途径的所有详细信息，它包含大量的C和D，而文件2只包含以C开头并具有唯一(最后列出的C，数目较少)的指定ID行。文件如下所示：

文件1:

C    00010 Glycolysis / Gluconeogenesis [PATH:smup00010]
D      SMPSPU_277 pfkA; 6-phosphofructokinase   K00850 pfkA; 6-phosphofructokinase 1 [EC:2.7.1.11]
D      SMPSPU_278 gapA; glyceraldehyde 3-phosphate dehydrogenase        K00134 GAPDH; glyceraldehyde 3-phosphate dehydrogenase [EC:1.2.1.12]
D      SMPSPU_274 acoA; pyruvate dehydrogenase E1 component subunit 
alpha       K00161 PDHA; pyruvate dehydrogenase E1 component alpha subunit 
[EC:1.2.4.1]
D      SMPSPU_172 korA; 2-oxoglutarate ferredoxin oxidoreductase subunit alpha  K00174 korA; 2-oxoglutarate/2-oxoacid ferredoxin oxidoreductase subunit alpha [EC:1.2.7.3 1.2.7.11]
D      SMPSPU_061 korB; 2-oxoglutarate ferredoxin oxidoreductase subunit beta   K00175 korB; 2-oxoglutarate/2-oxoacid ferredoxin oxidoreductase subunit beta [EC:1.2.7.3 1.2.7.11]
C    00020 Citrate cycle (TCA cycle) [PATH:smup00020]
D      SMPSPU_201 sucA; 2-oxoglutarate dehydrogenase, E1 component      K00164 OGDH; 2-oxoglutarate dehydrogenase E1 component [EC:1.2.4.2]
D      SMPSPU_120 lpdA; dihydrolipoamide dehydrogenase  K00382 DLD; dihydrolipoamide dehydrogenase [EC:1.8.1.4]
D      SMPSPU_172 korA; 2-oxoglutarate ferredoxin oxidoreductase subunit alpha  K00174 korA; 2-oxoglutarate/2-oxoacid ferredoxin oxidoreductase subunit alpha [EC:1.2.7.3 1.2.7.11]
D      SMPSPU_169 sucD; succinyl-CoA synthetase subunit alpha   K01902 sucD; succinyl-CoA synthetase alpha subunit [EC:6.2.1.5]
D      SMPSPU_229 pdhB; pyruvate dehydrogenase E1 component subunit beta        K00162 PDHB; pyruvate dehydrogenase E1 component beta subunit [EC:1.2.4.1]
D      SMPSPU_275 pdhC; dihydrolipoamide acyltransferase E2 component   K00627 DLAT; pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [EC:2.3.1.12]
C    00030 Pentose phosphate pathway [PATH:smup00030]
D      SMPSPU_057 tktB; transketolase, N-terminal subunit       K00615 E2.2.1.1; transketolase [EC:2.2.1.1]
D      SMPSPU_058 tktA; transketolase, C-terminal subunit       K00615 E2.2.1.1; transketolase [EC:2.2.1.1]
C    00051 Fructose and mannose metabolism [PATH:smup00051]
D      SMPSPU_277 pfkA; 6-phosphofructokinase   K00850 pfkA; 6-phosphofructokinase 1 [EC:2.7.1.11]
D      SMPSPU_230 fbaA; fructose-bisphosphate aldolase  K01624 FBA; fructose-bisphosphate aldolase, class II [EC:4.1.2.13]

文件2:

C    00261 Monobactam biosynthesis [PATH:smup00261]
C    00300 Lysine biosynthesis [PATH:smup00300]
C    00660 C5-Branched dibasic acid metabolism [PATH:smup00660]
C    00680 Methane metabolism [PATH:smup00680]
C    02020 Two-component system [PATH:smup02020]
C    02024 Quorum sensing [PATH:smup02024]

现在我只想提取文件2中存在的C和它们各自的D。

我试过这个剧本

fgrep -f name-C-non-homowba00001 wba00001.keg |grep -E '^C.*PATH|^D' | less

但是我给了我这个C id和名字文件。

Answer 1

试试这个：

cat input | grep -E '^[CD]' | sed -n '/^C.*PATH/,/^C/p' | uniq -f2 | grep -E '^C.*PATH|^D'

其中：

• input是您的文件
• first grep打印所有以C开头的行或以C开头的所有行，包含以C开头的所有行，包含以C开头的下一行，(included)
• uniq取消所有相等的相邻行，除了前两个字段之外，
• 最后grep打印以C开头的所有行，包含路径或以D

开头的行

Answer 2

awk '$1!~/^D$/ { select=0; } $1=="C" && $NF~/PATH/ { select=1; } {if(select) print; }' inputfile

解释：

$1!~/^D$/ { select=0; } ( D以外的行)停止输出。

$1=="C" && $NF~/PATH/ { select=1; } --在最后一个字段中包含PATH的C行开始输出。

如果选择用于输出的{if(select) print; }打印当前行。

Answer 3

这是一个安全的方法：

awk '(NR==FNR){a[$0];next}/^C/{p=($0 in a)}p' file2 file1