[EMBOSS] Seqret and Stdout

Ronnie O ronnieoc at gmail.com
Tue Oct 4 11:56:06 UTC 2005

Hello all,
I posted a bit ago about a problem I thought I was having piping data to
stdin using seqret. I have more thoroughly investigated my problem and I
have actually narrowed it down to getting my application to capture stdout
from seqret. Quite the opposite than my original idea, but I have learned
and debugged a lot since then! From posting previously, i took advice to
create and analyze the debug file. From looking at the dbg file, I can see
that my sequence data is making it into seqret and the dbg file appears
identical to one created if I run the following command from a terminal:
 cat testdna | ./seqret raw::stdin raw::stdout -filter -debug
 The sequence in file testdna is printed to the screen (stdout, i assume). I
have the same sequence data being piped in via a Cocoa application on mac os
x. Comparison of the dbg files shows that they are identical. From this
deduction, I assume in both cases data is being sent to stdout. Considering
all this, I was thinking the problem is the capturing of stdout by my cocoa
app. My problem with this idea is that I have the same exact piping
mechanism successfully capturing stdout from a perl script that just echoes
the data back.
 So my question to the forum, is there a possibility that the stdout from
seqret is being piped to dev/console or somewhere I could be missing it? I
also considered it was maybe being piped to stderror, but I have a pipe set
up to catch that too (which has successfully caught errors). I included the
-filter argument so the "read and writes sequences" output doesnt get
returned to my cocoa app, would this alter data output at all? Or can anyone
tell me how I could access the STDOUT environmental variable to make sure my
pipe call is resulting in data sent to stdout? I have debugged this with
both apps, and I have a tight area where things could be going wrong. Any
ideas? Thanks again to all!

More information about the EMBOSS mailing list