Re: Defining substring matches

[BrowserUk]

I wish to use the substr() function to search for the particular motif.

#

substr is *not* designed for (nor capable of) searching for anything; so why are you specifying that particular function?

You've defined your IUPAC codes in terms of regex character classes; so why are you eschewing the regex engine?

Given your table, it is trivial to convert IUPAC codes into a regex and use the regex engine to search your fasta file:

my %IUPAC = (
 A => '[A]',
 C => '[C]',
 G => '[G]',
 T => '[T]',
 R => '[AG]',
 Y => '[CT]',
 M => '[AC]',
 K => '[GT]',
 W => '[AT]',
 S => '[GC]',
 B => '[CGT]',
 D => '[AGT]',
 H => '[ACT]',
 V => '[ACG]',
 N => '[ACGT]',
);

my( $file, $motif ) = @ARGV;

my $re = join '', map $IUPAC{ $_ }, split '', $motif;

open FASTA, '<', $file or die $!;
getc( FASTA );                        ## discard first '>'
until( eof( FASTA ) ) {
    chomp( my $id = <FASTA> );                 ## read ident
    my $seq = do{ local $/ = '>'; <FASTA> };
    $seq =~ tr[\n>][]d;
    while( $seq =~ m[($re)]g ) {
        printf "Found: '$1' at '$id':%d\n", $-[0];
    }
}

NB: The above is untested code typed directly into my browser.