Mastering Perl for Bioinformatics [Electronic resources] نسخه متنی

A.13 Binding Operators

Binding operators
are used for pattern matching,
substitution, and transliteration on strings. They are used with
regular expressions that specify the patterns:

'ACGTACGTACGTACGT' =~ /CTA/

The pattern is the string CTA, enclosed by forward
slashes. The string binding operator is
=~; it tells the program which string
to search, returning true if the pattern appears
in the string.

!~ is another
string binding operator; it returns true if the
pattern isn't in the string:

'ACGTACGTACGTACGT' !~ /CTA/

This is equivalent to:

not 'ACGTACGTACGTACGT' =~ /CTA/

You can substitute one pattern for another
using the string binding operator. In the next example,
s/thine/nine/ is the substitution command, which
substitutes the first occurrence of thine with the
string nine:

$poor_richard = 'A stitch in time saves thine.';
$poor_richard =~ s/thine/nine/;
print $poor_richard;

This produces the output:

A stitch in time saves nine.

Finally, the
transliteration (or translate)
operator tr substitutes characters in a string. It
has several uses, but the two uses I've covered are
first, to change bases to their
complements A T, C G, G
C, and T A:

$DNA = 'ACGTTTAA';
$DNA =~ tr/ACGT/TGCA/;

This produces the value:

TGCAAATT

Second, the tr operator counts the number of a
particular character in a string, as in this example which counts the
number of Gs in a string of DNA sequence data:

$DNA = 'ACGTTTAA';
$count = ($DNA =~ tr/A//);
print $count;

This produces the value 3; it shows that a pattern match can return a
count of the number of translations made in a string, which is then
assigned to the variable $count.