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The first thing I’d say about this program is ... “always use real variables,” not “implied” stuff like $_ which can very easily get away from you.   Then, “start with a test case.” One example string, that you can verify gets correctly parsed by the regular-expression you intend to use.   You can even use a “Perl one-liner” like this:

perl -e 'my $str = "chr1:4777082-4777141"; \ my ($foo) = $str =~ /([0-9]+)/; print "foo is $foo\n";' foo is 1 ... oops, that's not right ... mike$ perl -e 'my $str = "chr1:4777082-4777141"; \ my ($foo) = $str =~ /[:]([0-9]+)/; print "foo is $foo\n";' foo is 4777082 ... correct.

Now, write your program, something like:

while (my $str = <INFILE>) { my ($foo) = $str =~ /[:]([0-9]+)/; # WE TESTED THIS die "Something's Wrong with $str!" unless ($foo); # NEVER ASSUME, NEVER ASSUME print OUTFILE "FILE=$foo\n"; # NOTICE DOUBLE-QUOTES }

We used the one-liners to verify the actual regular-expression parsing, to quickly get it right (and to uncover a subtle bug in the first attempt), then wrote code that is above all else, clear to do the actual work.

Within that program, we also added a die statement that will cause the program to test its assumption that every single record of the input will be handled correctly.   (We could make this test even-more aggressive if we knew that every record of the input file should contain seven digits, preceded by a ":" and followed by a "-", with: (see bold-faced parts)
/[:]([0-9]{7})[-]/)
Thus, the very fact that the program runs normally to completion, with a very stringent regular-expression that must be matched every time, is a strong indication that both the input data and the resulting output are correct.


In reply to Re: handling files using regular expression by sundialsvc4
in thread handling files using regular expression by rocketperl

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