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Извлечь значение из другого столбца и заменить в другом столбце

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Извлечь значение из другого столбца и заменить в другом столбце

Мне нужно сделать это:

##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

Заменить строки (Xm Gen CDS) значениями, присутствующими в строках (Xm Gen извлеченная область). Например, первая строка ($4 столбец:1 заменяется на значение 437225, а $5 столбец:148 заменяется на значение 437372, в строке 2 ($4 столбец:149 заменяется на значение 436969, $5 столбец:193 заменяется на значение 437013 и т. д.) и вывести вывод, как показано ниже.

##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

решение1

Немного сложный вариант, но работает довольно хорошо.

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

запустить его как скрипт оболочки

#!/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"

Связанный контент