quoting issue with system command

lomSpace has asked for the wisdom of the Perl Monks concerning the following question:

Replies are listed 'Best First'.
Re: quoting issue with system command by almut (Canon) on May 12, 2009 at 22:21 UTC
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?)	[reply] [d/l] [select]
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 $alignment);` [download]	[reply] [d/l] [select]
Re: quoting issue with system command by jwkrahn (Abbot) on May 12, 2009 at 22:32 UTC
Use a list instead of a string: `my @command = ( 'c:\\blast\bin\blastall', '-p', 'blastn', '-d', "$hu_s +eq $hd_seq", '-i', $contig, '-o', $alignment ); print "@command\n"; 0 == system @command or die "system @command failed: $?";` [download]	[reply] [d/l]
Re^2: quoting issue with system command (Win32) by tye (Sage) on May 13, 2009 at 00:02 UTC
Unfortunately, that doesn't work on Win32. Of course, I believe we should just fix that (though a bit of mushiness on how such things need to be quoted means that the fix wouldn't be foolproof, but I think it is clearly something Perl should try to do). To be specific, `system(@list)` on Win32 Perl is just the same as `system("@list")`, unfortunately. - tye	[reply] [d/l] [select]
Re^3: quoting issue with system command (Win32) by ikegami (Patriarch) on May 13, 2009 at 00:40 UTC
It works for me. `my $hu_seq = 'value of $hu_seq'; my $hd_seq = 'value of $hd_seq'; my $contig = 'value of $contig'; my $alignment = 'value of $alignment'; my @command = ( 'echo', '-leprint for @ARGV', '--', '-p', 'blastn', '-d', "$hu_seq $hd_seq", '-i', $contig, '-o', $alignment ); 0 == system @command or die "system @command failed: $?";` [download] >c:\progs\perl5100\bin\perl t.pl "-leprint for @ARGV" -- -p blastn -d "value of $hu_seq value of $hd_se +q" -i "value of $contig" -o "value of $alignment" >c:\progs\perl589\bin\perl t.pl "-leprint for @ARGV" -- -p blastn -d "value of $hu_seq value of $hd_se +q" -i "value of $contig" -o "value of $alignment" >c:\progs\perl580\bin\perl t.pl "-leprint for @ARGV" -- -p blastn -d "value of $hu_seq value of $hd_se +q" -i "value of $contig" -o "value of $alignment" >c:\progs\perl561\bin\perl t.pl "-leprint for @ARGV" -- -p blastn -d "value of $hu_seq value of $hd_se +q" -i "value of $contig" -o "value of $alignment" [download] Here's a version where what you said is true: `>c:\progs\perl560\bin\perl t.pl -leprint for @ARGV -- -p blastn -d value of $hu_seq value of $hd_seq - +i value of $contig -o value of $alignment` [download] (Switch `echo` for `$^X` for another view.) These are all ActivePerl builds.	[reply] [d/l] [select]
Re^4: quoting issue with system command (Win32) by tye (Sage) on May 13, 2009 at 00:56 UTC
Re^5: quoting issue with system command (Win32) by John M. Dlugosz (Monsignor) on May 13, 2009 at 20:49 UTC
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Re^4: quoting issue with system command (Win32) by almut (Canon) on May 13, 2009 at 01:41 UTC
Re^5: quoting issue with system command (Win32) by ikegami (Patriarch) on May 13, 2009 at 02:02 UTC
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Re^5: quoting issue with system command (echo.exe) by tye (Sage) on May 13, 2009 at 03:55 UTC
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Re: quoting issue with system command by John M. Dlugosz (Monsignor) on May 12, 2009 at 23:33 UTC
In general, you need to learn more about Perl strings and interpolation. You put `$contig` inside of single tick quotes, and that won't interpolate. Meanwhile, you wrote `">".$maid_dir."\\".$maid."_aln.out"` where you didn't interpolate where a Perl programmer normally would, even though you were using double-tick quotes! For comparison, `">$maid_dir\\${maid}_aln.out"` (notice how the last one was handled since it was immediately followed by a character allowed in an identifier). Meanwhile, use the 3-argument form of open. Don't concatenate the ">" with the name, but keep it as a separate argument. But, as another poster mentioned, passing the open file, stringified (whatever that does) to the blastall.exe command line doesn't make sense. You meant to pass the file name. `my $outfile= "$maid_dir\\${maid}_aln.out"; my $command= qq(c:\\blast\\bin\\blastall -p blastn -d "$hu_seq $hd_seq +" -i $contig +-o $alignment);` [download] Note the use of `qq(...)` instead of double-tick quotes, so I could use " characters inside the string without escaping them. That's probably why you used single-quotes there in the first place. I do like how you composed the command string separately to using it in the `system` command, so you could easily see what the command was. I don't know why you are putting quotes around the two file names together with a space in between, instead of quoting each file name individually. Something about that blastall.exe I suppose, if that's correct. But beware of `$maid_dir` containing spaces. —John	[reply] [d/l] [select]
Re^2: quoting issue with system command by lomSpace (Scribe) on May 13, 2009 at 15:42 UTC
I have to put quotes around the two filenames with a space in between to create the database. $contig is the query. Also, yes $maid_dir has can have spaces in it. What is the best way to get around that? LomSpace	[reply]
Re^3: quoting issue with system command by John M. Dlugosz (Monsignor) on May 13, 2009 at 16:02 UTC
Put the exe name in quotes, too: `"D:\Program Files\foo.exe" arg1 arg2 "file_name with spaces.txt"` [download] The logic of system's argument processing is supposed to make sense on Unix, with underlying OS primitives that work in the same way. But it's a mess on Windows, where the documented meaning is implemented to some degree. Point is, it takes different code paths depending on the form, with different behavior. It's been a while since I looked at it. But if it calls the CMD.exe shell with the whole thing as a string, it behaves the same way as on the command line, as I showed. If it tries to call CreateProcess directly, the exe file name is a separate argument to that. I suppose I should refresh my knowledge before writing anything that makes use of that feature myself.	[reply] [d/l]
Re^4: quoting issue with system command by lomSpace (Scribe) on May 13, 2009 at 17:46 UTC
Re^5: quoting issue with system command by ikegami (Patriarch) on May 13, 2009 at 18:14 UTC
Re^5: quoting issue with system command by John M. Dlugosz (Monsignor) on May 13, 2009 at 20:26 UTC
Re^4: quoting issue with system command by lomSpace (Scribe) on May 13, 2009 at 18:04 UTC