I'm pretty new to perl and I'm taking a metagenomics course; for our homework, we have to use regular expressions, take a fasta file and print out the sequence IDs, then state how many sequences were found. I've got the regex to find the right pattern and I can print all the right information out, but since my prof uses a tester to check all of our homework, if our output isn't exactly what he wants, it's wrong. For his expected output, he wants something like:

1: foo

2: bar

3: baz

Found 3 sequences.

I can do that, but I can't quite get my program to not print out the '>' in front of the sequence ID. My output right now looks like this:

1: >foo

2: >bar

3: >baz

Found 3 sequences.

How can I get it to not print out that '>'? Thanks for any help you can give!

#!/usr/bin/env perl
use strict;
use warnings;
use autodie;
use feature 'say';
my $i    = 0;
my $file = shift @ARGV;
my $pattern;
open my $fh, '<', $file;
while (my $line = <$fh>) {
        chomp $line;
        $pattern  = '>';
        if ($line =~ /^$pattern/) {
                $i++;
                print "$i: $line \n";
        }

}
printf "Found %s sequence%s.\n", $i, $i == 1 ? '' : 's';

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In reply to Pattern finding and printing with regex by kernelpanic@thedisco

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