[EMBOSS] Reading Two Sequences from stdin with water
Jan T. Kim
jtk at cmp.uea.ac.uk
Fri Jun 3 12:41:24 UTC 2005
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
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