needle -filter

[Peter Rice]

simon andrews (BI) wrote:
> 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?

EMBOSS (and anything else) expects one standard input.

You are trying to read 2 inputs from stdin. needle will accept one 
sequence from stdin and another from "somewhere else".

But you can do this:

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

EMBOSS treats "cat seq1.txt|" as a command and reads the standard output.

With -filter it will default to writing to stdout.

Hope this helps,

Peter Rice