You are almost there :-)
my ($helper1, $helper2);
my $counter = 1;
foreach my $line(@list){
chomp $line;
my @coordinates = split(/' '/, $region);
my $chromosome = $coordinates[0];
my $start = $coordinates[1];
my $end = $coordinates[2];
my $strand = $coordinates[3];
# Using a simple modulo operation (returns 1 if counter is an uneven
number and 0 otherwise
# you can simply decide the even and uneven lines on the uneven line
you capture the Chromosome and Start
# and on the even lines you capture the End and the Strand, as well as
printing out the result of the
# beginning of the previous line and the end of the current line.
#
# Using a for loop instead of a for each loop will result in a nicer
looking loop
# and it might (never actually tested this be a little bit faster as
well (benchmark that to be sure)
# which on large amounts of data as you are likely to be processing
might save you a
# decent bit of time.
if ( ! $counter % 2 ) { $helper1 = "$chromosome $start"; }
if ( $counter % 2 ) { $helper2 = "$end $strand"; print "$helper1
$helper2\n"; }
$counter++;
}
Hope that helps,
Rob
On Thu, May 12, 2011 at 11:23 AM, Nathalie Conte <n...@sanger.ac.uk> wrote:
>
> HI,
>
> I have this file format
> chr start end strand
> x 12 24 1
> x 24 48 1
> 1 100 124 -1
> 1 124 148 -1
>
> Basically I would like to create a new file by grouping the start of the
> first line (12) with the end of the second line (48) and so on
> the output should look like this:
> x 12 48 1
> 1 100 148 -1
>
> I have this script to split and iterate over each line, but I don't know
> how to group 2 lines together, and take the start of the firt line and the
> end on the second line? could you please advise? thanks
>
> unless (open(FH, $file)){
> print "Cannot open file \"$file\"\n\n";
> }
>
> my @list = <FH>;
> close FH;
>
> open(OUTFILE, ">grouped.txt");
>
>
> foreach my $line(@list){
> chomp $line;
> my @coordinates = split(/' '/, $region);
> my $chromosome = $coordinates[0];
> my $start = $coordinates[1];
> my $end = $coordinates[2];
> my $strand = $coordinates[3];
> ...???
>
>
>
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