Re^2: quoting issue with system command

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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]

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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);
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