needle -filter
Peter Rice
pmr at ebi.ac.uk
Mon Jun 9 16:09:09 UTC 2003
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
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