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Re: Running an external command

by Eldan Aranye (Acolyte)
on Apr 26, 2012 at 09:11 UTC ( #967274=note: print w/ replies, xml ) Need Help??


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;

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


Comment on Re: Running an external command
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Re^2: Running an external command
by ww (Bishop) 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."

Re^2: Running an external command
by Mr. Muskrat (Abbot) 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;

    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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