[EMBOSS] Seqret stdin issues

[Peter Rice]

Ronnie O wrote:

> Hi Peter,
> First, thanks for your reply and sorry for my delay.  I went with your
> suggestion of running seqret with the -debug flag set in hopes of
> finding something and heres what I came up with.
> 
> First, I first ran seqret from the command line with the following command:
> 
> ./seqret raw::testdna raw::stdout -filter -debug
> 
> I created a file, "testdna", that simply held nucleotide characters in
> raw format.  Execution was successful, as the sequence was output to
> the terminal window, and the seqret.dbg file was created in the emboss
> folder.
> 
> Second, I ran my cocoa application which calls seqret with basically
> the same sequence of flags with the exception of "stdin" for
> "testdna":
> 
> seqret raw::stdin raw::stdout -filter -debug
> 
> My application is not receiving data from seqret as of this point.

It will be waiting to read from stdin (waiting for you to type something).

You need to pipe the testdna file into the program, for example (depending on 
which shell you use):

cat testdna | seqret raw::stdin raw::stdout  -debug

(-filter is not needed as you are already writing to stdout - but it does no harm)

> Just to clarify too about the output of diff, I had it output only the
> lines that were different.  So all the other lines of the dbg files
> were identical.

That just shows the different input filename (stdin or testdna) and the first 
run succeeding. We need the seqret.dbg file froj a run that says something like:

  Unable to read sequence 'raw::stdin raw::stdout'
Died: seqret terminated: Bad value for '-sequence' and no prompt

to diagnose why it failed to read.

Good luck!

Peter