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別の列から値を抽出し、別の列に置き換える

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別の列から値を抽出し、別の列に置き換える

これをする必要があります:

##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

(Xm Gen CDS) 行を (Xm Gen 抽出領域) 行にある値に置き換えます。つまり、最初の行 ($4 列:1 は 437225 値に置き換えられ、$5 列:148 は 437372 に置き換えられ、2 行目では ($4 列:149 は 436969 に置き換えられ、$5 列:193 は 437013 に置き換えられるなど)、以下のように出力を印刷します。

##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

答え1

少し複雑なバリエーションですが、非常にうまく機能します。

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

シェルスクリプトとして実行する

#!/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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