Re: Query on Perl system command

[philipbailey]

It looks like a quoting problem. It seems that you want to interpolate your variable $filename within your quoted string but interpolation does not happen within Perl's single quotes.

There are several possibilities, but one would be to use double quotes, then escape the double quotes and "\n" you are using:

system "echo -e \"$filename.txt\\n$filename.xls\\n\" | phylip";

Also note that, on my system at least, I need the -e option to get backslash escapes to be interpreted.

[Anonymous Monk]

Thanks Philip Bailey.

I put up a simplified script in my query, but the actual script is different. It is given below. (Description of this script is in Re^4 above)

As suggested by you, I modified script

system 'echo "4\n6\n3\n5\n\n1\n$filename.fsmi\n5\n$filename.phb\n111\n
+1000\n4\n$filename.ph\n$filename.dst\n\n2\n" | phylip';

with

system "echo -e \"4\\n6\\n3\\n5\\n\\n1\\n\"$filename.fsmi\"\\n5\\n\"$f
+ilename.phb\"\\n111\\n1000\\n4\\n\"$filename.ph\"\\n\"$filename.dst\"
+\\n\\nx\\n\" | phylip" ;

I did not get any error message, but, none of the choices are recognized

I appreciate your help, thank you

[Eliya]

Have you also tried without the -e option?  Not all echos require that option, and in the other thread it looks like your echo doesn't.

Another approach would be to do away with system, echo, quoting issues, etc. and use open to open a pipe to phylip, into which you then just print the required input, including newlines.  For example:

open my $pipe, "| phylip" or die $!;

print $pipe <<"EOI";
4
6
3
5

1
$filename.fsmi
5
$filename.phb
111
1000
4
$filename.ph
$filename.dst

x
EOI

close $pipe;

A positive side effect is that the sequence of things you have to enter becomes much better to read.

(Note that the heredoc, as shown, is interpolating $filename (like a double-quoted string). )

[Anonymous Monk]

Thank you Eliya :-)
Yes, you are right, open command is much easier to read and it works perfectly well.
Chak