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Dear PerlMonks,

I'm having an issue with printing long strings. I build an array of 251 elements and join it with \t to print to a file. The problem is that the output randomly misses \t 's and sometimes both the \t and the last letter of the previous value.

I've tried using autoflush and printflush but the problems remain. Any suggestion would be much appreciated. This is the problem line at the moment:

$normal_fh->printflush(join("\t",@arrayToPrint)."\n");
[download]

UPDATED: Here is the code I am using

    open my( $normal_fh ), ">>", $normalOut or die("Couldn't open NORM
+AL $normalOut $!\n");
    my @arrayToPrint;
    if ($nbGABlocks == 0) {
        @arrayToPrint = ();
        #print ("NoAlignmentBlocks!\n");
        my @subArray = ($chrInterval,$startInterval,$endInterval,"NA",
+"NA","NA");
        my @naArray = ("NA","NA","NA","NA","NA","NA","NA") x scalar(@s
+pecies);
        push(@arrayToPrint,@subArray);
        push(@arrayToPrint,@naArray);
    }
    NORMALBLOCK: foreach my $block (sort{$blocksHash{$a}{"orderBlock"}
+ <=> $blocksHash{$b}{"orderBlock"}} keys %blocksHash) {
        my $spNb = 0;
        my $order = $blocksHash{$block}{"orderBlock"};
        @arrayToPrint = ();
        my @subArray = ($chrInterval,$startInterval,$endInterval,$bloc
+k,$order,$warning);
        push(@arrayToPrint,@subArray);
        @subArray = ();
        SP: foreach my $sp (@species) {
            my $newSp = $speciesCorrespond{$sp};
            $spNb++;
            if (exists($blocksHash{$block}{$newSp})) {
                my $chr = $blocksHash{$block}{$newSp}{"chr"};
                my $start = $blocksHash{$block}{$newSp}{"start"};
                my $end = $blocksHash{$block}{$newSp}{"end"};
                my $strand = $blocksHash{$block}{$newSp}{"strand"};
                my $size = $blocksHash{$block}{$newSp}{"sizeBlock"};
                my $comment = $spBlocksHash{$newSp}{$block}{"comment"}
+;
                @subArray = ($newSp,$chr,$start,$end,$strand,$size,$co
+mment);
                push(@arrayToPrint,@subArray);
                @subArray = ();
            } else {
                @subArray = ($newSp,"NA","NA","NA","NA","NA","NA");
                push(@arrayToPrint,@subArray);
                @subArray = ();
            }
        }
        my $printing = join("\t",@arrayToPrint);
        $" = "\t";
        $normal_fh->printflush("$printing\n");
    }
[download]

The output is very long, but here is a sample, where you can see that for some lines, instead of getting: spermophilus_tridecemlineatus\tNA, I get spermophilus_tridecemlineatuNA:

rattus_norvegicus    NA    NA    NA    NA    NA    NA    dipodomys_ord
+ii    NA    NA    NA    NA    NA    NA    spermophilus_tridecemlineat
+us    NA    NA    NA    NA    NA    NA    ochotona_princeps    NA    
+NA    NA    NA    NA    NA    oryctolagus_cuniculus    NA    NA    NA
+    NA    NA    NA
rattus_norvegicus    5    13171176    13038994    -1    132183    NotC
+ontiguous_326154Gap    dipodomys_ordii    NA    NA    NA    NA    NA 
+   NA    spermophilus_tridecemlineatus    NA    NA    NA    NA    NA 
+   NA    ochotona_princeps    NA    NA    NA    NA    NA    NA    ory
+ctolagus_cuniculus    NA    NA    NA    NA    NA    NA
rattus_norvegicus    NA    NA    NA    NA    NA    NA    dipodomys_ord
+ii    NA    NA    NA    NA    NA    NA    spermophilus_tridecemlineat
+uNA    NA    NA    NA    NA    NA    ochotona_princeps    NA    NA   
+ NA    NA    NA    NA    oryctolagus_cuniculus    NA    NA    NA    N
+A    NA    NA
rattus_norvegicus    NA    NA    NA    NA    NA    NA    dipodomys_ord
+ii    NA    NA    NA    NA    NA    NA    spermophilus_tridecemlineat
+uNA    NA    NA    NA    NA    NA    ochotona_princeps    NA    NA   
+ NA    NA    NA    NA    oryctolagus_cuniculus    NA    NA    NA    N
+A    NA    NA
rattus_norvegicus    5    13004812    12917777    -1    87036    NotCo
+ntiguous_253399Gap    dipodomys_ordii    NA    NA    NA    NA    NA  
+  NA    spermophilus_tridecemlineatus    NA    NA    NA    NA    NA  
+  NA    ochotona_princeps    NA    NA    NA    NA    NA    NA    oryc
+tolagus_cuniculuNA    NA    NA    NA    NA    NA
rattus_norvegicus    5    12917776    12899724    -1    18053    Conti
+guous    dipodomys_ordii    NA    NA    NA    NA    NA    NA    sperm
+ophilus_tridecemlineatus    NA    NA    NA    NA    NA    NA    ochot
+ona_princeps    NA    NA    NA    NA    NA    NA    oryctolagus_cunic
+ulus    NA    NA    NA    NA    NA    NA
[download]

Thanks a lot for your help,

Sophie.

In reply to Missing \t in print output by Sophienz

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