[EMBOSS] Reading Two Sequences from stdin with water

[Jan T. Kim]

Dear EMBOSSers,

is it possible to read both input sequences to a pairwise alignment
from one input stream?

With the test input file attached, the command

    water -asequence fasta::x.fasta:seq1 -bsequence fasta::x.fasta:seq2 -outfile stdout -auto

runs as I expect, but the command

    cat x.fasta | water -asequence fasta::stdin:seq1 -bsequence fasta::stdin:seq2 -outfile stdout -auto

gives

   EMBOSS An error in ajfile.c at line 1926:
Error reading from file 'stdin'

It may well be that water consumes the entire input stream on getting the
first sequence, thus rendering itself unable to acquire the second one.

Is there a solution to this? I would really like to avoid the mess of
temporary files and run water in a clean pipe (pun intended  ;-)  )

Best regards & thanks in advance, Jan
-- 
 +- Jan T. Kim -------------------------------------------------------+
 |    *NEW*    email: jtk at cmp.uea.ac.uk                               |
 |    *NEW*    WWW:   http://www.cmp.uea.ac.uk/people/jtk             |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*
-------------- next part --------------
> seq1
accaacc
> seq2
acgagcc