needle -filter

[simon andrews (BI)]

I'm trying to get needle to work from a set of sequences held in memory, rather than have it pick up its input from a file.  For something like seqret I can do:

cat seq.txt | seqret -filter -osf fasta | more

and seqret will read in on stdin and write out on stdout.

In the manual for needle it suggests that it too can accept -filter as a qualifier, but I can't get it to work.  

cat seq1.txt seq2.txt | needle -filter -sformat1 fasta -sformat2 fasta

It always dies with the message "Bad option for -seqall with -auto defined".  I'm trying to feed it two concatenated fasta files as input, but when I debug it it looks like it only gets one of them.

Does anyone have any suggestions as to how I can make this work?

	Cheers

	Simon.

--
Simon Andrews PhD
Bioinformatics Dept
The Babraham Institute

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