[EMBOSS] Seqret stdin issues
Ronnie O
ronnieoc at gmail.com
Thu Sep 15 22:45:10 UTC 2005
Hello everyone,
I am trying to pipe sequence data into seqret via a pipe with the following
command:
./seqret raw::stdin raw::stdout
and i am getting the following data piped back to my app via the error
pipe:
Unable to read sequence 'raw::stdin raw::stdout'
Died: seqret terminated: Bad value for '-sequence' and no prompt
I am new to using the EMBOSS package and am not familiar with the errors.
So is this a standard error for telling me that my input is not recognized
or formatted correctly? This is confusing me b/c I am piping this sequence
data in the same manner to a perl script it is being recognized correctly. I
am just sending a sample string of "ATGCATGC". The perl script spits it back
to me through:
$data = <STDIN>; //The dna string also has a \n added for the perl stdin
which I've removed for stdin to seqret
print $data;
So I am hesitant to think my piping mechanism isn't sufficient, but rather
seqret is looking for some other flags for stdin or a different formatting.
Any ideas?
Thanks,
Ronnie
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