Call console command and return as string...problem

ruby-talk
1

Hi,

I am trying to use the following line of code in a rails application,
but I dont think my problem has anything to do with rails, but with
ruby, so this is why I post it here. To set the scene - I am programming
an application for biological sequence analysis (among other things...).

I want to pass the contents of an array (DNA sequences) to an external
program. This program, however, needs a file as input and doesnt seem to
take input from STDIN (its written in C so I have no clue how to mess
with its code to change that..).
So instead I write the sequences into a file and pass the name to the
program. So far so good. But if I run it like this

@result = %x{program-executable -o infile.txt}

the variable @result is empty (should be a string, right?). If I call
the exact same command from the command line, it prints the output to
the screen, so I figured that it should go into the @result variable,
no?

Any suggestions on what I am doing wrong? Also, if by chance, anybody
has an idea on how to pass the variable to the program instead of going
via the route with a physical file, I'd be glad to hear it.

Cheers,
Marc

···

--
Posted via http://www.ruby-forum.com/.

2

Hi,

I am trying to use the following line of code in a rails application,
but I dont think my problem has anything to do with rails, but with
ruby, so this is why I post it here. To set the scene - I am programming
an application for biological sequence analysis (among other things...).

I want to pass the contents of an array (DNA sequences) to an external
program. This program, however, needs a file as input and doesnt seem to
take input from STDIN (its written in C so I have no clue how to mess
with its code to change that..).
So instead I write the sequences into a file and pass the name to the
program. So far so good. But if I run it like this

@result = %x{program-executable -o infile.txt}

the variable @result is empty (should be a string, right?). If I call
the exact same command from the command line, it prints the output to
the screen, so I figured that it should go into the @result variable,
no?

The command seems fine. Parameter -o seem suspicious since it is
usually used for output.
Anyway, I guess this is an exception.

Try redirecting stderr to either file (2> errr.log) or to stdout
(2>&1, works even on windows!) to
see if there are any errors.

Any suggestions on what I am doing wrong? Also, if by chance, anybody
has an idea on how to pass the variable to the program instead of going
via the route with a physical file, I'd be glad to hear it.

See IO.popen and/or Open3.popen3

···

On Tue, Apr 8, 2008 at 3:14 PM, Marc Hoeppner <marc.hoeppner@molbio.su.se> wrote:

3

That kind of depends on the executable you're running.

if you do @results = %x{ls} what do you get (assuming you're on a unix)

Julian.

Learn Ruby on Rails! Check out the FREE VIDS (for a limited time) VIDEO #3 out NOW!
http://sensei.zenunit.com/

···

On 08/04/2008, at 11:14 PM, Marc Hoeppner wrote:

Hi,

I am trying to use the following line of code in a rails application,
but I dont think my problem has anything to do with rails, but with
ruby, so this is why I post it here. To set the scene - I am programming
an application for biological sequence analysis (among other things...).

I want to pass the contents of an array (DNA sequences) to an external
program. This program, however, needs a file as input and doesnt seem to
take input from STDIN (its written in C so I have no clue how to mess
with its code to change that..).
So instead I write the sequences into a file and pass the name to the
program. So far so good. But if I run it like this

@result = %x{program-executable -o infile.txt}

the variable @result is empty (should be a string, right?). If I call
the exact same command from the command line, it prints the output to
the screen, so I figured that it should go into the @result variable,
no?

Any suggestions on what I am doing wrong? Also, if by chance, anybody
has an idea on how to pass the variable to the program instead of going
via the route with a physical file, I'd be glad to hear it.

Cheers,
Marc
--
Posted via http://www.ruby-forum.com/\.