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I am a biologist, I need one more help in text file editing. I would like to get the help of computer experts

##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
share|improve this question
    
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). –  Gilles Jul 3 '12 at 23:42
    
Just to add to @Gilles's comment, here is a reference for editing –  Levon Jul 4 '12 at 0:40

1 Answer 1

up vote 2 down vote accepted

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"
share|improve this answer
    
It would be great..if there is any perl script from the computer experts –  jack Jul 5 '12 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. –  jack Jul 5 '12 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. –  rush Jul 5 '12 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 –  jack Jul 5 '12 at 19:54
    
Unfortunately I'm not good enough in perl. May be someone else will help you. –  rush Jul 5 '12 at 20:10

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