Re: Pattern Match Issue

If I assume that your posted code ends with two closing curly brackets, I see a clear issue. The while(<$fh>){ structure splits your file based upon the record separator, which is new line by default. Since you haven't set it ($/), that means your code is first getting fed ">CIMG_12545 | Coccidioides immitis RS hypothetical protein (translation) (95 aa)" on the first loop iteration and then "MSSQPTTLQSQTGIQRHGEISSQAQKPTTALEEDDEFEDFPVEDWPQEDAEALGPAGTNN" on the second. Therefore, you can't match across the new lines. If you want to look for patterns across new lines, you either need to slurp your file ($/) or modify your while loop to read in more than one line in an iteration (plus many other possible variations on the theme). So something like this might work:

use strict;
use warnings;

local $/;
my ($name, $aa);

while (my $seq = <DATA>) {
    if ($seq =~ />(\w+).+aa\)\n(\w+)/m) {
        $name = $1;
        $aa = $';
    }
}

print "$name $aa\n";
__DATA__
>CIMG_12545 | Coccidioides immitis RS hypothetical protein (translatio
+n) (95 aa)
MSSQPTTLQSQTGIQRHGEISSQAQKPTTALEEDDEFEDFPVEDWPQEDAEALGPAGTNN
DHLWEESWDDDDSNEEFSRQLKEELKKVEAMKQQ*
[download]

A side note, while (my $seq = <$IN2>) { is a bad structure to get into the habit of using, since it will exit your loop if the line evaluates to false - i.e. if you have a blank line in your file. Better would be while (defined (my $seq = <$IN2>)) {. See almut below.

Update: I should mention that for what you've written the m modifier on your regular expression has no impact. As it states in Modifiers, m modifies the matching behavior of ^ and $ so they match new lines. You don't have either metacharacter in your expression, so the modifier is unnecessary.

Comment on Re: Pattern Match Issue Select or Download Code

Replies are listed 'Best First'.
Re^2: Pattern Match Issue by almut (Canon) on Nov 23, 2009 at 21:24 UTC
... Better would be `while (defined (my $seq = <$IN2>)) {` AFAIK, current versions of Perl implicitly do this anyway: `#!/usr/bin/perl open my $IN2, "<", "foo.txt" or die; while (my $seq = <$IN2>) { print "line: '$seq'\n"; }` [download] `$ perl -MO=Deparse ./808927.pl die unless open my $IN2, '<', 'foo.txt'; while (defined(my $seq = <$IN2>)) { print "line: '${seq}'\n"; } ./808927.pl syntax OK` [download] It's only when you write things like `while (chomp(my $seq = <$IN2>))` that you run into problems... (because chomp returns the number of characters removed, which may be zero for the last line if it doesn't contain a `"\n"`)	[reply] [d/l] [select]

Replies are listed 'Best First'.

Re^2: Pattern Match Issue
by almut (Canon) on Nov 23, 2009 at 21:24 UTC

... Better would be while (defined (my $seq = <$IN2>)) {

AFAIK, current versions of Perl implicitly do this anyway:

#!/usr/bin/perl

open my $IN2, "<", "foo.txt" or die;

while (my $seq = <$IN2>) {
    print "line: '$seq'\n";
}
[download]

$ perl -MO=Deparse ./808927.pl
die unless open my $IN2, '<', 'foo.txt';
while (defined(my $seq = <$IN2>)) {
    print "line: '${seq}'\n";
}
./808927.pl syntax OK
[download]

It's only when you write things like while (chomp(my $seq = <$IN2>)) that you run into problems... (because chomp returns the number of characters removed, which may be zero for the last line if it doesn't contain a "\n")

[reply]
[d/l]
[select]