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从不同列中提取值并替换到另一列中

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从不同列中提取值并替换到另一列中

我需要这样做：

##fsdfsd
##sdd-ver gen 5.5.7
Xm Gen CDS     1       148     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen CDS     149     193     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen CDS     194     279     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen CDS     280     412     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen CDS     413     499     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen CDS     500     702     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen extracted region        1       148     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="437225 <- 437372";ID=Bm
Xm Gen extracted region        149     193     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="436969 <- 437013";ID=Bm
Xm Gen extracted region        194     279     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="435418 <- 435503";ID=Bm
Xm Gen extracted region        280     412     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="435209 <- 435341";ID=Bm
Xm Gen extracted region        413     499     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="434376 <- 434462";ID=Bm
Xm Gen extracted region        500     702     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="434084 <- 434286";ID=Bm

将 (Xm Gen CDS) 行替换为 (Xm Gen 提取区域) 行中存在的值。即第一行（$4 列：1 替换为 437225 值，$5 列：148 替换为 437372，在第 2 行中（$4 列：149 替换为 436969，$5 列：193 替换为 437013 等等）并打印输出，例如以下

##gff-version 2
##source-version geneious 5.5.7
Xm Gen CDS     437225       437372     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen CDS     436969     437013     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen CDS     435418     435503     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen CDS     435209     435341     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen CDS     434376     434462     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen CDS     434084     434286     .       +       .       Name=;created by=User;modified by=User;ID=Bm
Xm Gen extracted region        1       148     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="437225 <- 437372";ID=Bm
Xm Gen extracted region        149     193     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="436969 <- 437013";ID=Bm
Xm Gen extracted region        194     279     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="435418 <- 435503";ID=Bm
Xm Gen extracted region        280     412     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="435209 <- 435341";ID=Bm
Xm Gen extracted region        413     499     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="434376 <- 434462";ID=Bm
Xm Gen extracted region        500     702     .       +       .       Name=Extracted region from gi|371442828|gb|JH557032.1|;Extracted interval="434084 <- 434286";ID=Bm

答案1

有点复杂的变体，但效果很好。

head -2 file 
join <(grep "Xm Gen CDS" file | cat -n) \
     <(grep "Xm Gen extracted region" file | cat -n) | \
     sed 's/^[0-9]* //;s/CDS [0-9]*\s[0-9]*\(\s.*interval="\([0-9]*\)\s<-\s\([0-9]*\)\)/CDS\t\2\t\3\t\1/;s/ Xm Gen extracted.*//'
grep "Xm Gen extracted region" file

将其作为 shell 脚本运行

#!/bin/bash
FILE="$1"
head -2 "$FILE"
join <(grep "Xm Gen CDS" "$FILE" | cat -n) \
     <(grep "Xm Gen extracted region" "$FILE" | cat -n) | \
     sed 's/^[0-9]* //;s/CDS [0-9]*\s[0-9]*\(\s.*interval="\([0-9]*\)\s<-\s\([0-9]*\)\)/CDS\t\2\t\3\t\1/;s/ Xm Gen extracted.*//'
grep "Xm Gen extracted region" "$FILE"

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