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
use strict;
use warnings;
my %first_start;
while (<>) {
next if /^chr/; # skip header line
chomp;
my ($chr, $start, $end, $strand) = split;
if ( exists $first_start{$chr} ) {
print "$chr $first_start{$chr} $end $strand\n";
}
else {
$first_start{$chr} = $start;
}
}
Put this in a file, "combine-chromosomes" for example
and then:
perl combine-chromosomes infile.txt >grouped.txt
Hope it helps
- Pete
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