How I can take the coordinates of a block of numbers? - perl

Question

I have a problem tha bothers me a lot...
I have a file with two columns (thanks to your help in a previous question) like:
14430001 0.040
14430002 0.000
14430003 0.990
14430004 1.000
14430005 0.050
14430006 0.490
....................
the first column is coordinates the second probabilities.
I am trying to find the blocks with probability >=0.990 and to be more than 100 in size.
As output I want to be like this:
14430001 14430250
14431100 14431328
18750003 18750345
.......................
where the first column has the coordinate of the start of each block and the second the end of it.
I wrote this script:
use strict;
#use warnings;
use POSIX;
my $scores_file = $ARGV[0];
#finds the highly conserved subsequences
open my $scores_info, $scores_file or die "Could not open $scores_file: $!";
#open(my $fh, '>', $coords_file) or die;
my $count = 0;
my $cons = "";
my $newcons = "";
while( my $sline = <$scores_info>) {
my #data = split('\t', $sline);
my $coord = $data[0];
my $prob = $data[1];
if ($data[1] >= 0.990) {
#$cons = "$cons + '\n' + $sline + '\n'";
$cons = join("\n", $cons, $sline);
# print $cons;
$count++;
if($count >= 100) {
$newcons = join("\n", $newcons, $cons);
my #array = split /'\n'/, $newcons;
print #array;
}
}
else {
$cons = "";
$count = 0;
}
}
It gives me the lines with probability >=0.990 (the first if works) but the coordinates are wrong. When Im trying to print it in a file it stacks, so I have only one sample to check it.
Im terrible sorry if my explanations aren't helpful, but I am new in programming.
Please, I need your help...
Thank you very much in advance!!!

Answer 1

You seem to be using too much variables. Also, after splitting the array and assigning its parts to variables, use the new variables rather than the original array.
sub output {
my ($from, $to) = #_;
print "$from\t$to\n";
}
my $threshold = 0.980; # Or is it 0.990?
my $count = 0;
my ($start, $last);
while (my $sline = <$scores_info>) {
my ($coord, $prob) = split /\t/, $sline;
if ($prob >= $threshold) {
$count++;
defined $start or $start = $coord;
$last = $coord;
} else {
output($start, $last) if $count > 100;
undef $start;
$count = 0;
}
}
output($start, $last) if $count > 100;
(untested)