Reading two lines in a while loop and combining the lines

Shell Programming and Scripting
1

Dear all,
I have a file like this:
imput

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:

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:

while read line1
do
    read line2
    echo $line1 $line2
done < imput

But the results is:

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.

2

Could I suggest something like:-

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

1 Like
3

Try:

{ read line1   
  while read line2
  do
    printf "%s\t%s\n" "$line1" "$line2"
    line1=$line2
  done
} < imput
4

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. :o

Robin

5

Hi,

another way;

cat YUORFILE.txt | awk -F" " '{ if (  FNR == 1  ) {a=$0;getline} ;  {print a"\t"$0;a=$0} }'
1 Like
6

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

@Robin, your suggestion look fine, I think it is more a matter of preference. Not every echo interprets a \t like that btw...