Re^3: Writing to file...

Thanks for all the help so far guys!
One last question: I have this code trying to capture the locus name and place it after the ">" but nothing I do lets me capture it.

    while (<$in>) 
    {
        my $locus =~ /LOCUS\s+(\w+)/;           
        s/\^\^/>$locus\n^^\n/g;
        print $out $_;

    }
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within the file the Locus name is formatted like this

Created: Tuesday, July 12, 2005 4:14 PM
LOCUS       AJ877264                 704 bp    DNA     linear   INV 15
+-APR-2005
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Re^4: Writing to file... by Marshall (Canon) on Jul 24, 2009 at 22:24 UTC
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/^\sLOCUS\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 [download]	[reply] [d/l]

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Re^4: Writing to file...
by Marshall (Canon) on Jul 24, 2009 at 22:24 UTC

#!/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
[download]

[reply]
[d/l]