Perl: string formatting in tab delimited file - perl

Question

I have no background in programming whatsoever, so I would appreciate it if you would explain how and why any code you recommend should be written the way it is.
I have a data matrix 2,000+ samples, and need to do the following manipulate the format in one column.
I would also like to manipulate the format of one of the columns so that it is easier to merge with my other matrix. For example, one column is known as sample number (column #16). The format is currently similar to ABCD-A1-A0SD-01A-11D-A10Y-09, yet I would like to change it to be formatted to the following ABCD-A1-A0SD-01A. This will allow me to have it in the right format so that I can merge it with another matrix. I seem to not be able to find any information on how to proceed with this step.
The sample input should look like this:
ABCD-A1-A0SD-01A-11D-A10Y-09
ABCD-A1-A0SD-01A-11D-A10Y-09
ABCD-A1-A0SE-01A-11D-A10Y-09
ABCD-A1-A0SE-01A-11D-A10Y-09
ABCD-A1-A0SF-01A-11D-A10Y-09
ABCD-A1-A0SH-01A-11D-A10Y-09
ABCD-A1-A0SI-01A-11D-A10Y-09
I want the last three extensions removed. The output sample should look like this:
ABCD-A1-A0SD-01A
ABCD-A1-A0SD-01A
ABCD-A1-A0SE-01A
ABCD-A1-A0SE-01A
ABCD-A1-A0SF-01A
ABCD-A1-A0SH-01A
ABCD-A1-A0SI-01A
Finally, the matrix that I want to merge with has a different layout, in other words the number of columns and rows are different. This is a issue when I tackle the next step which is merging the two matrices together. The original matrix has about 52 columns and 2,000+ rows, whereas the merging matrix only has 15 column and 467 rows.
Each row of the original matrix has mutational information for a patient. This means that the same patient with the same ID might appear many times. The second matrix contains the patient information, so no patients are repeated in that matrix. When merging the matrix, I want to make sure that every patient mutation (each row) is matched with its corresponding information from the merging matrix.
My sample code:
#!/usr/bin/perl
use strict;
use warnings;
my $file = 'sorted_samples_2.txt';
open(INFILE, $file) or die "Can't open file: $!\n";
open(my $outfile, '>', 'sorted_samples_changed.txt');
foreach my $line (<INFILE>) {
print "The input line is $line\n";
my #columns = split('\t', $line);
($columns[15]) = $columns[15]=~/:((\w\w\w\w-\w\d-\w|\w\w-\d\d\w)+)$/;
printf $outfile "#columns/n";
}
Issues: The code deletes the header and deleted the string in column 16.

Answer 1

A few issues about your code:
Good job on include use strict; and use warnings;. Keep doing that
Anytime you're doing file or directory processing, include use autodie; as well.
Always use lexical file handles $infh instead of globs INFILE.
Use the 3 parameter form of open.
Always process a file line by line using a while loop. Using a for loop loads the entire file into memory
Don't forget to chomp your input from a file.
Use the line number variable $. if you want special logic for your header
The first parameter of split is a pattern. Use /\t/. The only exception to this is ' ' which has special meaning. Currently your introducing a bug by using a single quoted string.
When altering a value with a regex, try to focus on what you DO want instead of what you DON'T. In this case it looks like you want 4 groups separated by dashes, and then truncate the rest. Focus on matching those groups.
Don't use printf when you mean print.
The following applies these fixes to your script:
#!/usr/bin/perl
use strict;
use warnings;
use autodie;
my $infile = 'sorted_samples_2.txt';
my $outfile = 'sorted_samples_changed.txt';
open my $infh, '<', $infile;
open my $outfh, '>', $outfile;
while (my $line = <$infh>) {
chomp $line;
my #columns = split /\t/, $line;
if ($. > 1) {
$columns[15] =~ s/^(\w{4}-\w\d-\w{4}-\w{3}).*/$1/
or warn "Unable to fix column at line $.";
}
print $outfh join("\t", #columns), "\n";
}

Answer 2

You need to define scope for your variables with 'my' in declaration itself when you use 'use strict'.
In your case, you should use my #sort = sort {....} in first line and
you should have an array reference $t defined somewhere to de-reference it in second line. You don't have #array declared anywhere in this code, that is the reason you got all those errors. Make sure you understand what you are doing before you do it.