Hello PerlMonks!
I have a wierd problem. I am able to read the file, process it, and print to a file only
when I include the data in the script using __DATA__. When I read into the IN
filehandle and write to an out file I get a blank file. Any Ideas?
The following is the code:

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

#open file for reading
open(IN,"/Users/me/Desktop/CCDS.current.txt") or die " Can't open file
+: $!";
#open out file for writing
open(OUT, ">/Users/me/Desktop/withdrawndata.txt");
#remove the header
my $firstline= <IN>;
chomp $firstline;
while(<IN>){
    chomp; # remove the newline character
    my @fields = split/\t/; # split the file into columns where eachli
+ne in it 
    #populates and array for that column.
    if($fields[5] =~ m/Withdrawn/){ # print eachline that has "Withdra
+wn" in field[5]
        print  OUT "$_\n"; # print to file 
    }
}
close(IN);
close(OUT); 
__DATA__
#chromosome    nc_accession    gene    gene_id    ccds_id    ccds_stat
+us    cds_strand    cds_from    cds_to
1    NC_000001.8    NCRNA00115    79854    CCDS1.1    Withdrawn    -  
+  801942    802433
1    NC_000001.10    SAMD11    148398    CCDS2.2    Public    +    861
+321    879532
1    NC_000001.10    NOC2L    26155    CCDS3.1    Public    -    88007
+3    894619
1    NC_000001.10    PLEKHN1    84069    CCDS4.1    Public    +    901
+911    909954
1    NC_000001.10    HES4    57801    CCDS5.1    Public    -    934438
+    935352
1    NC_000001.10    ISG15    9636    CCDS6.1    Public    +    948953
+    949857
1    NC_000001.10    C1orf159    54991    CCDS7.2    Public    -    10
+18272    1026922
1    NC_000001.10    TTLL10    254173    CCDS8.1    Public    +    111
+5433    1120521
1    NC_000001.10    TNFRSF18    8784    CCDS9.1    Public    -    113
+8970    1141950
1    NC_000001.10    TNFRSF18    8784    CCDS10.1    Public    -    11
+39223    1141950
1    NC_000001.10    TNFRSF4    7293    CCDS11.1    Public    -    114
+6934    1149506

[download]

Your wisdom is appreciated!
LomSpace

In reply to Where is my output stream to a file going? by lomSpace

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