Re: Pattern finding and printing with regex

A more general solution is to write your regex to find the sequence ID rather than removing the '>' character.

$pattern = qr/^(\w*)/;
if ($line =~ /$pattern/) {
    my $id = $1;
    $I++;
    print "$i: $id \n";
}
[download]

This approach would exclude the optional sequence description if it were included in the fasta file.

UPDATE: AnomalousMonk is correct. I accidentally omitted the '<' from my regex.

Bill

Comment on Re: Pattern finding and printing with regex Download Code

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Re^2: Pattern finding and printing with regex by AnomalousMonk (Archbishop) on Oct 22, 2015 at 01:33 UTC
But `qr/^(\w)/` won't capture anything — or more precisely, it will match and capture the empty string. Maybe try something like `qr/^>(\w)/` instead: `c:\@Work\Perl\monks>perl -wMstrict -le "my $line = '>CATCATCATCAT'; ;; my $pattern = qr/^>(\w*)/; if ($line =~ /$pattern/) { my $id = $1; print qq{got: '$id'}; } " got: 'CATCATCATCAT'` [download] Give a man a fish: `<%-{-{-{-<`	[reply] [d/l] [select]