Piping with emboss utilites that expect two files as input

Estienne Swart estienne at sanbi.ac.za
Mon Sep 9 09:53:43 UTC 2002


Is there any way to directly pipe two sequences into utitilities such as 
water/matcher, etc. which require usually require two files as input? It 
is possible to pipe one or the other (seqA or seqB, e.g.water -auto 
-filter -SeqA sample1.seq < sample2.seq  ), but no both at once 
(e.g.water -auto -filter < sample1.seq < sample2.seq ).

I know not all shells can read from multiple pipes(?), like zsh can, e.g.:

cat < sample2.seq <sample1.seq

 >A less simple sequence
 >A simple sequence

But, it will really be useful (from a scripting perspective) if these 
utilities could at least take a pair of sequences from stdin, and align 

Estienne Swart

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