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Full Discussion: Need help comparing Base Pairs within PERL
Top Forums Shell Programming and Scripting Need help comparing Base Pairs within PERL Post 302652165 by ddreggors on Thursday 7th of June 2012 09:24:38 AM
Old 06-07-2012
I found the issue.
See my above comment... I updated it to show what I did.

---------- Post updated at 04:09 PM ---------- Previous update was at 03:31 PM ----------

Actually, now that we have solved the original code... there is a better way to do this.
Here is a way smaller piece code that removes the need for second array (@ref) and I nest the loops.

Code:
#!/usr/bin/perl


use strict;
use warnings;
my (@data, $tmpidx, $tmpref);
open(FILE1,"<","file1.txt") or die $!;
while (<FILE1>) {
        chomp;
        next unless $_ =~ /^\d/;
        @data =  split(/\s+/,$_);
        open(FILE2,"<","file2.txt") or die $!;
        while (<FILE2>) {
                /^(\d*)\s*([a-z]*)/i;
                $tmpidx = $1;
                $tmpref = $2;
                next unless $_ =~ /^\d/;
                next unless $data[0] == $tmpidx;
                next unless $data[87] =~ /$tmpref/i;
                print $data[0] . "\t" . $data[5] . "\t" . $data[87] . "\n";
        }
        close FILE2;
}
close FILE1;


Result:
Code:
[user@host ~]$ ./test3.pl    
4       Exonic  AA
5       Intronic        GC

---------- Post updated 06-07-12 at 09:24 AM ---------- Previous update was 06-06-12 at 04:09 PM ----------

OK, after a bit more tweaking, here is the smallest and cleanest I could get the code.


Code:
#!/usr/bin/perl

use strict;
use warnings;
my (@ref, @data, $refidx, $ref, $row, @dataline, $refline);
open(FILE1,"<","file1.txt") or die $!; @data = <FILE1>; close(FILE1);
open(FILE2,"<","file2.txt") or die $!; @ref = <FILE2>; close(FILE2);
foreach $row (@data) {
        next unless $row =~ /^\d/;
        foreach $refline (@ref) {
                next unless $refline =~ /^\d/;
                ($refidx, $ref) = split('\s*', $refline);
                @dataline = split('\s',$row);
                next unless $dataline[0] == $refidx;
                next unless $dataline[87] =~ /$ref/i;
                print $dataline[0] . "\t" . $dataline[5] . "\t" . $dataline[87] . "\n";
        }
}

It weighs in at 18 lines, the files are read into arrays and closed immediately.
This User Gave Thanks to ddreggors For This Post:
drossy
 

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set_color

set_color(1)							       fish							      set_color(1)

NAME

       set_color - set_color - set the terminal color

set_color - set the terminal color
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   Description
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