Analyzing a txt list in perl [closed] - perl

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I am trying to analyze a list of coordinates. The txt file is set up like this:
ID START END
A 10 20
B 15 17
C 20 40
How would I check this dataset to check if START and END is included within a user-specified region, e.g. START=10 END=15?
Any help greatly appreciated
// edit //
if(#AGRV != 4) {
print STDOUT "Searches genomic data for CNV within range. \n";
print STDOUT "CNV FILE FORMAT: <ID><CHR>BPS><BPE><AGE><etc...> \n";
print STDOUT "USAGE: [CNVLIST][CHR][BPS][BPE][OUTFILE] \n";
exit;
}
open(CNVLIST,"<$ARGV[0]");
open(OUTFILE,">$ARGV[3]");
$BPS = $ARGV[1];
$BPE = $ARGV[2];
#put CNV file in hash table
$line = <CNVFILE>;
while($line = <CNVFILE>) {
chomp $line;
($Cchr,$CS,$CE,$CID) = split(/\t/,$line);
}
I need to look through each line and find if the start/end lies within the user specified range.

Answer 1

it is unclear whether you can assume that the ID will never overlap with each other, but assuming it won't , you can use hash to store the lines that are within the range. If it's possible that the ID might overlap, I think you can push #{$result{id}}, [$start, $end]; but that'll make the data structure a bit more complicated.
#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
my $in_file = "input.txt";
# User-specified region
my $range_start = 10;
my $range_end = 15;
open my $fh, $in_file or die $!;
my %result;
while (<$fh>) {
my ($id, $start, $end) = split " ", $_;
next unless $start =~ /\d/;
# Swap if START is larger than END
($start, $end) = ($end, $start) if $start > $end;
$result{$id} = [$start, $end]
if $start >= $range_start and $end <= $range_end;
}
print Dumper(%result);

Answer 2

You can split() each line and check second and third field:
#!/usr/bin/env perl
use strict;
use warnings;
my ($start, $end) = (shift, shift);
die if $start > $end;
## Skip header
<>;
while ( <> ) {
chomp;
my #f = split;
if ( $f[1] <= $start && $f[2] >= $end ) {
printf qq|%s\n|, $_;
}
}
It accepts three arguments, the first one is the start region, the second one is the end region and the last one is the file to process. It prints to output all lines that pass the condition.
Run it like:
perl script.pl 10 15 infile
That yields:
A 10 20