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Need help comparing Base Pairs within PERL

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# 15  
Old 06-06-2012
when I make the change to '=~' i get the following errors:

Code:
 
Use of uninitialized value $1 in concatenation (.) or string at ddreggors.pl line 26, <FILE2> line 5.
Use of uninitialized value $1 in array element at ddreggors.pl line 26, <FILE2> line 5.
Use of uninitialized value in concatenation (.) or string at ddreggors.pl line 26, <FILE2> line 5.
Use of uninitialized value $1 in concatenation (.) or string at ddreggors.pl line 26, <FILE2> line 6.
Use of uninitialized value $1 in array element at ddreggors.pl line 26, <FILE2> line 6.
Use of uninitialized value in concatenation (.) or string at ddreggors.pl line 26, <FILE2> line 6.


Do you know what could be causing this?
Thanks again
# 16  
Old 06-06-2012
can you send me your code, or at minimum line 26 of your code?

---------- Post updated at 03:21 PM ---------- Previous update was at 03:19 PM ----------

Is that all you have changed?
When you change it back it works?

---------- Post updated at 03:27 PM ---------- Previous update was at 03:21 PM ----------

Never mind I see it....

I had to assign the 2 reference file columns to a variable and use the variable then it it works. Somehow after the match line $1 was getting unset, so the print line was failing on $1.

Code:
#!/usr/bin/perl


use strict;
use warnings;
my ($idx, $tmp, @data);
open(FILE1,"<","file3.txt") or die $!;
while (<FILE1>) {
        chomp;
        next unless $_ =~ /^\d/;
        ($idx, $tmp) = split(/\s+/,$_,2);
        $data[$idx] = $tmp;
}
open(FILE2,"<","file2.txt") or die $!;
while (<FILE2>) {
        chomp;
        next unless $_ =~ /^\d/;
        /^(\d*)\s*([a-z]*)/i;
        my @tmparr = split(/\s+/,$data[$1]);
        my $tmpref = $2;
        my $tmpidx = $1;
        next unless $tmparr[86] =~ /$tmpref/;
        print $tmpidx . "\t" . $tmparr[4] . "\t" . $tmparr[86] . "\n";
}

# 17  
Old 06-06-2012
This is what it currently is:

Code:
#!/usr/bin/perl


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

# 18  
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
# 19  
Old 06-07-2012
Thank you so much that is working great for me and I really appreciate the help.
Hopefully one my last questions but I now have a similar situation but the data and reference are both in the same file. For example:


Code:
Column 1     ....        Column 6     .....   Column 88      Column 89
(Index)                   (mutation)            (Genotype)      Reference
1                             Intronic                 TT                 A
2                             Frameshift             GT                 C
3                             Exonic                   AT                 C
4                             Exonic                   AA                 A
5                             Intronic                 GC                 G

So now rather than comparing the data to column 2 in another file, I would like to compare it to column 89 of the same file.
Is there a quick fix for this?
Thanks again!
# 20  
Old 06-07-2012
That is actually easier and least memory/disk intensive.

Here is a quick modification (untested) that should work...

Code:
#!/usr/bin/perl

use strict;
use warnings;
my (@data, $row, @dataline);
open(FILE1,"<","file1.txt") or die $!; @data = <FILE1>; close(FILE1);
foreach $row (@data) {
        next unless $row =~ /^\d/;
        @dataline = split('\s',$row);
        next unless $dataline[87] =~ /$dataline[88]/i;
        print $dataline[0] . "\t" . $dataline[5] . "\t" . $dataline[87] . "\n";
}

If you have any issues let me know and I will change as needed.
# 21  
Old 06-07-2012
That program appears to be running but no output is given when it is written as above. Do you know what could have happened?
thanks
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