[EMBOSS] Seqret stdin issues

[Ronnie O]

Thanks guys,
Luke, the first suggestion was definitely a fix. I separated the arguments 
into two individual items in an array of arguments that is sent to the 
command line. I originally was sending the entire line "raw::stdin 
raw::stdout" as one item. This change deleted my error of:
 Unable to read sequence 'raw::stdin raw::stdout'
Died: seqret terminated: Bad value for '-sequence' and no prompt
 So that was definitely an issue.
 Second, Simon, I also can run the command:
 echo "GATA" | ./seqret raw::stdin raw::stdout
 in a terminal with success. To test succesful piping of stdin from my app 
(which is a Cocoa app), I wrote a simple perl script to print a variable 
that has been initialized to <STDIN>. This all functions correctly. I am not 
familiar with modules you mentioned, but the success of the simple perl 
script seems to tell me that I am correctly piping data out of the cocoa 
app, as well as receiving it correctly from stdout. Seqret is responding 
otherwise, as I am not getting data echoed back to my app at all. Whether 
this is due to stdin or stdout, I have yet to deduce. For the time being, I 
am going to make sure my cocoa code is up to par (which the perl script 
seems to be telling me it is), and I will probably re-post once I narrow it 
down to a seqret issue. Unless anyone has any cocoa-specific/seqret piping 
suggestions? Thanks a lot, fellas!
.........
Ronnie