This glob thing is just a mess. Part of the reason is the spaces that are allowed in some Windows file systems as you have noted! Youch! I beat the doo-doo out of an Active State app trying to get glob to work. Some of the modules worked with DOS glob and some with BSD glob.  use File::Glob 'glob'; is not a magic cure all. This BSD vs Sys V thing is weirder to understand. Anyway, I've spent many hours in "glob hell" and I just don't do it anymore.

Yes, closedir is the "right thing to do"! Every file handle comes from a limited pool of system resources. For a 20 line program, I don't worry about it much, but as they say "your mileage may vary". If this 20 line thing is in a client-server app, well then an open file handle here and there adds up! And the application bombs!

I tutor some students at a local college and one fundamental mistake is lack of whitespace and separating "thought units", but you see that too!

I have ammended my evil 'C' ways in favor of lining up braces. I am quite sure that this is the best way and I don't understand why you don't think that it is.

Anyway I say Horray! The OP has some good code to work from and I think he/she will do a great job!

glob is not that portable (BSD,DOS,Windows,SYS V), it is a mess. I prefer readdir and grep over glob.

In what respect? As long as you are using forward slashes for your pathes (in particular important if you are on Windows and dealing with UNC pathes), the fine thing about glob is that it works the same on all platform, since it doesn't rely on platform specific issues. At least this is true for any "reasonably recent" Perl; I darkly remember that for very early versions of Perl, glob used the shell mechanism on some platforms, which led to compatibility problems ... but this was long time ago.

Ronald, I would beg to differ. Glob can be a real mess. grep and readdir works on all platforms.

The forward vs backslash is not an issue. Perl'ers take note: always use "/" instead of some convoluted "\\" idea for a Windows path. Perl will translate the "/" into the right thing for Windows.

Update:
There are plenty of "old" Perl 5.6 programs out there! I skipped 5.8 and went to 5.10, so I don't know what 5.8 does. The glob mess that exists in 5.6 is gonna be around for a long time.

Glob can be a real mess.

Could you give a concrete example? If this is the case, I would conclude that this is a bug to be reported. From doc:://File::Glob:

File::Glob::bsd_glob() implements the FreeBSD glob(3) routine, which is a superset of the POSIX glob() (described in IEEE Std 1003.2 "POSIX.2"). bsd_glob() takes a mandatory "pattern" argument, and an optional "flags" argument, and returns a list of filenames matching the pattern, with interpretation of the pattern modified by the "flags" variable. Since v5.6.0, Perl's CORE::glob() is implemented in terms of bsd_glob().

-- 
Ronald Fischer <ynnor@mm.st>

Try adding quotes as follows:

foreach my $file ( grep{/\.seq$/ && -f "$dir/$_"}readdir DIR)
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Yes, toolic is right, without the quotes, this looks like a division. my goof. Typo's happen.

    
while (<$in>) 
    {
        if $in =~ /^^/  {
           s/\^\^/\n^^/g;
        print $out $_;
        else {
           s/[a]|[c]|[t]|[g]{6}/^^\n

    }
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The ^ character has meaning within a regex (anchor the following stuff at the beginning of line). If you want this ^ character be interpreted without the contextual meaning, ie literally, you need to "escape it" with a "\".

I'm not really sure what you are trying to do here. A simple example with a)I have this "X" and b)I what that "Y" would be helpful. BTW:

 
[a]|[c]|[t]|[g]{6} #looks like a char set 
[actg]{6}
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    while (<$in>) 
    {
        my $locus =~ /LOCUS\s+(\w+)/;           
        s/\^\^/>$locus\n^^\n/g;
        print $out $_;

    }
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Created: Tuesday, July 12, 2005 4:14 PM
LOCUS       AJ877264                 704 bp    DNA     linear   INV 15
+-APR-2005
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I am unsure as to what you want. But using the single line that you have give as input, here are several ways to extract the 2nd thing past the "LOCUS" name:

#!/usr/bin/perl -w
use strict;

my $in = "LOCUS       AJ877264                 704 bp    DNA     linea
+r   INV 15-APR-2005";
my $other_in = "    LOCUS AJ877264  ";

#===================
# this is a bit "tricky"...$locus is in a list context
# if you don't do that then you get True/False value of
# the match

my ($locus) = ($in=~ m/LOCUS\s+(\w+)/);
print "LOCUS=$locus\n";

#PRINTS:
#LOCUS=AJ877264

#==============
# this does the same thing with spaces in front of LOCUS
# in other words, no change is needed...
my ($other_locus) = ($other_in=~ m/LOCUS\s+(\w+)/);
print "LOCUS=$other_locus\n";

#PRINTS:
#LOCUS=AJ877264

#=================
# if you want to guarantee that the LOCUS you match is
# the first on on line preceded by some possible blanks, 
# my ($other_locus) = ($other_in=~ m/^\s*LOCUS\s+(\w+)/);
# will do it ^ start at beginning of line, then zero or
# blanks, then LOCUS, then one or more blanks then a 
# sequence of "word" characters [0-9A-Za-z_]+

#===================
# This is a "list slice". 
# split(/\s+/,$in) is put into a list context with ()
# and the second thing, index [1] is moved to lvalue

my $locus_also = (split(/\s+/,$in))[1];
#note "my ($locus_also) =" is also completely fine.
print "Another way: LOCUS=$locus_also\n";

#PRINTS:
#Another way: LOCUS=AJ877264

#===============
# the split version won't work with spaces in front
# of LOCUS as a "" list element will be created:

($locus_also) = (split(/\s+/,$other_in))[1];
print "Another way 2: LOCUS=$locus_also\n";

#PRINTS:
#Another way 2: LOCUS=LOCUS

($locus_also) = (split(/\s+/,$other_in))[2];
print "Another way 2: LOCUS=$locus_also\n";

#PRINTS:
#Another way 2: LOCUS=AJ877264

#=================
#or remove leading spaces, for the split case
$other_in =~ s/\s*//;
($locus_also) = (split(/\s+/,$other_in))[1];
print "Another way 2: LOCUS=$locus_also\n";

#PRINTS:
#Another way: LOCUS=AJ877264
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