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I need to do this:

##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

Replace (Xm Gen CDS) rows with values present in (Xm Gen extracted region) rows. i.e first row ($4 column:1 is replaced with 437225 value and $5 column:148 is replaced with 437372, in row 2 ($4 column:149 replaced with 436969, $5 column:193 replaced with 437013 and so on) and print output like below

##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
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  • Please take some time to read the editing help (click on the yellow ? on the top right of the question editor). In particular, indent data snippets with four spaces in the editor (use the code button or press Ctrl+K). Commented Jul 3, 2012 at 23:42
  • Just to add to @Gilles's comment, here is a reference for editing Commented Jul 4, 2012 at 0:40

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A little bit complicated variant, however it works pretty well.

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

to run it as a shell script

#!/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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  • It would be great..if there is any perl script from the computer experts Commented Jul 5, 2012 at 14:25
  • Great use of join & grep. Can you please tell me, how to run this as shell script, getting input from user and giving output. Commented Jul 5, 2012 at 15:07
  • @bioman just copy the second part to a script file, make it executable with chmod +x scriptname and execute as ./scriptname file_with_data. Commented Jul 5, 2012 at 19:10
  • thanks.Is it possible to get perl code. Because Xm Gen CDS line may differ as (eg.Ym Genx CDS) in various formats, so I cannot use grep Commented Jul 5, 2012 at 19:54
  • Unfortunately I'm not good enough in perl. May be someone else will help you. Commented Jul 5, 2012 at 20:10

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