How to escape additional empty line while parsing pairwise data in Perl

Question

I have an input file that looks like this:

>Seq_1;1
AAAAAAAAAAAAAAAAAAAAA
>Seq_2;1
CCCCCCCCCCCCCCCCCCCCC

And there are many more pairwise line like that. What I want to do is to simply print it out like this:

>Seq_1;1 AAAAAAAAAAAAAAAAAAAAA
>Seq_2;1 CCCCCCCCCCCCCCCCCCCCC

But why this code fail:

#!/usr/bin/perl -w

   while ( <> ) {
        chomp;
        my $line = $_;
        my $rdn = "";
        my $sq  = "";

        if ( $line =~ /^>/ ) {
            $rdn = $line;
        }
        elsif ($line =~ /^[ATCG]/) {
            $sq = $line;
        }

         print "$rdn $sq\n";

    }

It print this instead:

>Seq_1;1
 AAAAAAAAAAAAAAAAAAAAA
>Seq_2;1
 CCCCCCCCCCCCCCCCCCCCC

Answer 1

Since your data is 'pairwise', and unless you want to explicitly check each line for the patterns you describe, why not just read two lines at a time? Then do your processing:

#!/usr/bin/perl

use strict;
use warnings;


while (my $line1 = <>) {
    my $line2 = <>;

    chomp $line1;
    chomp $line2;

#   ...do_something...

    print "$line1 $line2\n";
}

Results:

>Seq_1;1 AAAAAAAAAAAAAAAAAAAAA
>Seq_2;1 CCCCCCCCCCCCCCCCCCCCC

Answer 2

This awk could make it:

$ awk '/^>/ {getline a; print $0,a}' file

it loads in the variable a the next line of the ones starting with >. Then prints both together.

Test

$ cat file
>Seq_1;1
AAAAAAAAAAAAAAAAAAAAA
>Seq_2;1
CCCCCCCCCCCCCCCCCCCCC
$ awk '/^>/ {getline a; print $0,a}' file
>Seq_1;1 AAAAAAAAAAAAAAAAAAAAA
>Seq_2;1 CCCCCCCCCCCCCCCCCCCCC

Answer 3

Because you're reading the file line by line and printing on every line? You probably want something more like this. Storing the value of the first line in the first iteration, then printing it out on the second interation. Note this code is by no means the best, as if your file isn't exactly like you've posted above it will almost certainly print the incorrect thing.

#!/usr/bin/perl -w

   my $rdn = "";

   while ( <> ) {
        chomp;
        my $line = $_;    
        if ( $line =~ /^>/ ) {
            $rdn = $line;
            next;
        }
        elsif ($line =~ /^[ATCG]/) {
            my $sq = $line;
            print "$rdn $sq\n";
        }    
    }

Answer 4

In each iteration, you set either $rdn or $sq, never both. Then you print both of them (one of them always "") with a \n at the end.

Try this, the idea being to only chomp off the \n if it's an even-numbered line, in that case printing a space instead:

my $lineno = 0;
while (<>) {
   if ($lineno % 2 == 0) {
      chomp;
      print $_, " ";
   } else {
      print;
   }
   $lineno++;
}