needle -filter

[Peter Rice]

David Mathog wrote:
>>Peter Rice wrote:
>>needle "cat seq1.txt|" "cat seq2.txt|" -sformat1 fasta -sformat2 fasta
> 
> That's got to be one of the ugliest syntaxes for reading 
> in two files I've ever seen!

It's standard in perl :-)

Any file ending in a pipe character is a command producing standard output.

>  Plus I don't understand how
> it differs from:
> 
>   needle seq1.txt seq2.txt

Because you don't have to use cat ... you can use seqret, getz, or 
anything else :-)

> It might be possible on some platforms to come up with a
> "firstfasta" filter program which would emit just the 
> first fasta entry from the stream.

That's already in EMBOSS several times, for example:

nthseq
seqret -first
skipseq -skip 1

SRS, to quote one example, uses these to split inputs.

> What Simon needs, and what Emboss doesn't have, is a built in
> splitter for multisequence files that will allow the individual
> sequences to be directed to specific inputs in a program like
> needle.

You mean needle seq1.txt:abc seq2.txt:xyz

That is already available!!!!

> For a program to compare one to many there could also be:
> 
>   -route 1:1,2-END:2

That would make workflows extremely messy.

I reckon the existing EMBOSS syntax covers everything perfectly well.

Hope this helps,

Peter