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Reading two lines in a while loop and combining the lines

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# 1  
Old 04-19-2012
Reading two lines in a while loop and combining the lines
Dear all,
I have a file like this:
imput
Code:
scaffold_0 1
scaffold_0 10000
scaffold_0 20000
scaffold_0 25000
scaffold_1 1
scaffold_1 10000
scaffold_1 20000
scaffold_1 23283

and I want the output like this:
Code:
scaffold_0 1         scaffold_0 10000
scaffold_0 10000 scaffold_0 20000
scaffold_0 20000 scaffold_0 25000
scaffold_0 25000 scaffold_1 1
scaffold_1 1         scaffold_1 10000
scaffold_1 10000 scaffold_1 20000
scaffold_1 20000 scaffold_1 23283

NOTE: I want the columns separated by tab

In other words, I want to combine
line 1 with line 2
line 2 with line3
line 3 with line4
....

I have this script:
Code:
while read line1
do
    read line2
    echo $line1 $line2
done < imput

But the results is:
Code:
scaffold_0 1         scaffold_0 10000
scaffold_0 20000 scaffold_0 25000
scaffold_1 1         scaffold_1 10000
scaffold_1 20000 scaffold_1 23283

so the script read line 1 and line 2, combine them, but do not follow reading the line 2 and combining with line 3. The script like jump the line 2 and follow the combination of line 3 and line 4 and again jump the next line (line 4).
How can I fix this script?

Best regards.
Moderator's Comments:
Mod Comment How to use code tags
Last edited by Scrutinizer; 04-19-2012 at 01:16 PM..
# 2  
Old 04-19-2012
Could I suggest something like:-
Code:
prev=""
while read line
do
   if [ "$prev" != "" ]
   then
      echo "$prev\t$line"
   fi
   prev="$line"
done < imput

The plan here being that for each line, you echo the previous line and the current read line, except for the first line read (where there is no previous)


I hope that this helps



Robin
Liverpool/Blackburn
UK
This User Gave Thanks to rbatte1 For This Post:
valente
# 3  
Old 04-19-2012
Try:
Code:
{ read line1   
  while read line2
  do
    printf "%s\t%s\n" "$line1" "$line2"
    line1=$line2
  done
} < imput

# 4  
Old 04-19-2012
Yes, that's neater. Sorry for being a fool and adding an if that will cost CPU especially for a large file. I wasn't thinking. Smilie




Robin
# 5  
Old 04-19-2012
Hi,

another way;
Code:
cat YUORFILE.txt | awk -F" " '{ if (  FNR == 1  ) {a=$0;getline} ;  {print a"\t"$0;a=$0} }'

This User Gave Thanks to pokerino For This Post:
valente
# 6  
Old 04-19-2012
Thanks Robin, It is nice to have smart guys like you in computer.
I'm a newbie in programming, in fact I'm a biologist that is entering in bioinformatics.
So I have two question,
when I insert
prev=""
while read line do
is it meaning that the prev="" will be the current line when the loop start?
The condition:
if [ "$prev" != "" ]meaning what?

Sorry to disturb your work.

Best regards.
# 7  
Old 04-19-2012
@Robin, your suggestion look fine, I think it is more a matter of preference. Not every echo interprets a \t like that btw...
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