[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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