I haven't read your other question. But you're about half-way there. If @output holds the data that you want saved, you next need to do something like this:

open my $out_fh, '>', 'filename.txt' or die $!;
print $out_fh @output;
close $out_fh or die $!;
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That's a simple means. But you'll probably need to modify it to better suit your needs, which weren't really fully described in this thread.

perlintro will take about a half hour to read. One of the sections in that document contains a brief introduction to file input and output.

If your program output a file, why use a backtick? simply use a open function in Perl, like this:

use warnings;
use strict;

my $output_file="output.bam";
open my $fh,'>',$output_file or die "can't open $output_file:$!";
   print $fh " ... hello world into my file...";
close $fh or die "can close file: $!";
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What did you try and how did it fail to meet your expectations?

open FILE,"< generatedFile.txt" or die "cant able to read file
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or

@output = `/home/.../samtools view...`
@fileout = `cat file.txt 2>&1`;
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This works only in unix

Actually, I ran this:

open INP,"< $ARGV[0]"
        or die "Cannot open file: $!";

$file = "$ARGV[1]";

open OUT, "> $file"
        or die "Cannot open file: $!";

@out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] 
+2>&1`;

print OUT @out;

close INP;
close OUT;
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And I was able to produce a non-empty file. Unfortunately, it got truncated somehow. Is it because of my use of backticks?

If the file referred to by $ARGV[1] should be appended to instead of overwritten then use the following code. Since you aren't actually using INP, I've removed it.

$file = "$ARGV[1]";

open OUT, ">> $file"
        or die "Cannot open file: $!";

@out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] 
+2>&1`;

print OUT @out;

close OUT;
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A better way to write that is shown below. The top three lines assume that this is a standalone script which it may not be.

#!/usr/bin/perl
use strict;
use warnings;

use autodie;

my $file = $ARGV[1];

open my $out, '>>', $file;

my @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[
+0] 2>&1`;

print $out @out;

close $out;
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Almost certainly, no.

But I, for one, need a more precise description of the problem than "...truncated somehow."