in reply to Running an external command

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;

[download]

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

Replies are listed 'Best First'.
Re^2: Running an external command
by Mr. Muskrat (Canon) on Apr 26, 2012 at 17:19 UTC

    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;

    [download]

    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;

    [download]
[reply]
[d/l]
[select]
Re^2: Running an external command
by ww (Archbishop) on Apr 26, 2012 at 11:45 UTC
    Almost certainly, no.

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

[reply]

In Section Seekers of Perl Wisdom