Re: quoting issue with system command

You probably intended to interpolate those variables (single quotes don't):

my $command = qq(c:\\blast\\bin\\blastall -p blastn -d "$hu_seq $hd_se
+q" -i $contig -o $alignment);
[download]

OTOH, interpolating the file handle $alignment doesn't make much sense... (so what is that -o $alignment supposed to achieve?)

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Re^2: quoting issue with system command by lomSpace (Scribe) on May 12, 2009 at 23:07 UTC
-o mean print results to an output file. In this case that is $alignment.	[reply]
Re^3: quoting issue with system command by almut (Canon) on May 12, 2009 at 23:15 UTC
but `$alignment` is a Perl file handle (that you explicitly opened), and you can't pass Perl file handles to other programs via `system()` arguments... Maybe you just want to pass the respective output filename instead (the one you used in the open())? `... my $alignment = "$maid_dir\\${maid}_aln.out"; my $command = qq(c:\\blast\\bin\\blastall -p blastn -d "$hu_seq $hd_se +q" -i $contig -o $alignment);` [download]	[reply] [d/l] [select]