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:

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

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';
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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" ;
[download]

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

I appreciate your help, thank you

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;
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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). )

$filename =~ s/\.doc$//;
qq(echo "$filename.txt\n$filename.xls\n" | phylip );
qq~echo "$filename.txt\n$filename.xls\n" | phylip ~;
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When I modified
system 'echo "$filename.txt\n$filename.xls\n" | phylip';

with

qq(echo "$filename.txt\n$filename.xls\n" | phylip );

OR with

qq~echo "$filename.txt\n$filename.xls\n" | phylip ~;

I get the following error message

"Useless use of string in void context at alignment.pl line 75."

Any idea, why this is happening ? (I am newbie to perl)

I appreciate your help

I'm a newbie to your code.

Which is / what's in "Line 75?"

You wrote

qq(echo "$filename.txt\n$filename.xls\n" | phylip );
qq~echo "$filename.txt\n$filename.xls\n" | phylip ~;
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Your script would have been

system qq(echo "$filename.txt\n$filename.xls\n" | phylip );
system qq~echo "$filename.txt\n$filename.xls\n" | phylip ~;
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I made a mistake by running your script blindly, so it didn't work that time. Yes you are right, single quotes do not interpolate, I needed double quotes !

Thank you :-)

I bet your phylip program asks the uses to type the first filename, reads the name in, asks for the second filename, etc.

Instead, make the program read the command line arguments it is invoked with, after which you can run it as

system( '/path/to/phylip', "$filename.txt", "$filename.xls" );
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You COULD have the program name and arguments all as one string, but then the shell is invoked to interpret things. With an array of args to system(), the program is invoked wthout involving the shell. That means you don't have to worry about the possibility of $filename having the value ';rm -rf'.