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Re^2: Running an external command

by Mr. Muskrat (Canon)
on Apr 26, 2012 at 17:19 UTC ( #967408=note: print w/replies, xml ) Need Help??

in reply to Re: Running an external command
in thread Running an external command

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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