Hi all,

I'm very new to Perl and am working on a Bioinformatics project at University. I have FILE1 containing a list of positions, in the format: 

 
99269
550
100
126477 
1700

[download]

And FILE2 in the format:

517 1878 forward
700 2500 forward
2156 3289 forward
99000 100000 forward
22000 23000 backward

[download]

I want to compare every position in FILE1 to every range in values on FILE2, and if a position falls into one of the ranges then i want to print the position, range and direction.

So my expected output would be:

99269 99000 100000 forward
550 517 1878 forward
1700 517 1878 forward

[download]

Currently it will run with no errors, however it doesn't output any information so i am unsure where i am going wrong! When i split the final 'if' rule it runs but will only work if the position is on exacly the same line as the range.

Any help would be much appreciated.

I have posted the same question on Stackoverflow as i'm after a fairly urgent answer.

My code is as follows:

 

#!/usr/bin/perl 

use strict;
use warnings;

my $outputfile = "/Users/edwardtickle/Documents/CC22CDS.txt"; 

open FILE1, "/Users/edwardtickle/Documents/CC22positions.txt" 
    or die "cannot open > CC22: $!";
    
open FILE2, "/Users/edwardtickle/Documents/CDSpositions.txt" 
    or die "cannot open > CDS: $!";    

open (OUTPUTFILE, ">$outputfile") or die "Could not open output file: 
+$! \n";

while (<FILE1>) {
    if (/^(\d+)/) {
    my $CC22 = $1;    
        
        while (<FILE2>) {
        if (/^(\d+)\s+(\d+)\s+(\S+)/) {
        my $CDS1 = $1;
        my $CDS2 = $2;
        my $CDS3 = $3;
    
            if ($CC22 > $CDS1 && $CC22 < $CDS2) {
                print OUTPUTFILE "$CC22 $CDS1 $CDS2 $CDS3\n";
                    }
                }
            }
        }
    }
    
close(FILE1);
close(FILE2);

[download]

In reply to Comparing FILE1 value to FILE2 range and printing matches by edwardtickle

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