[EMBOSS] Seqret stdin issues

[simon andrews (BI)]

On 15 Sep 2005, at 23:45, Ronnie O wrote:

> 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'

A simple pipe of the type you describe works fine for me:

echo "GATAGCTAG" | seqret raw::stdin fasta::stdout
Reads and writes (returns) sequences
 >EMBOSS_001
GATAGCTAG

However it sounds like you're trying to do this via a Perl script.  Are 
you using the IPC::Open2 / Open3 modules to do this?  I tried it and it 
seemed to work OK:

#!/usr/bin/perl
use warnings;
use strict;
use IPC::Open2;

my $seq = "GATAGATATGCTAGA";
my $pid = open2(\*OUT,\*IN,"seqret","raw::stdin","raw::stdout");

print IN $seq;
close IN or die "Can't close IN: $!";

while (<OUT>) {
   print;
}

close OUT or die "Can't close OUT: $!";
waitpid($pid,0);
##################

Incidentally, it you're just using seqret as a filter then there is a 
-filter flag which has a slightly cleaner syntax for what you're trying 
to do:

echo "GATAGCTAG" | seqret -filter -osf fasta

If you're still having problems then can you post the piece of code 
which isn't working so we can have a look.

Cheers

Simon.

-- 
Simon Andrews PhD
Bioinformatics Dept.
The Babraham Institute

simon.andrews at bbsrc.ac.uk
+44 (0) 1223 496463