[EMBOSS] Command line with --firstonly

[Peter Rice]

Peter Rice wrote:
> Niels Larsen wrote:
>> Have I overlooked a way to switch fasta output to sequence-as
>> -single-line mode? I think it allowed by fasta format, and
>> if I/we were to build a processing pipe with sequence flowing,
>> then I imagine that would be useful both for speed and I/O
>> simplicity ..
> 
> -ossingle

Oops. I misread your request as "single file mode".

If you want the sequence all on one line after the header that can be 
done, but would need a new format name... or more than one new name if 
you want to allow more than one style of ID.

Human chromosome 1 would have a very long line in the file.

In C I am not sure it helps with speed for long sequences ... EMBL 
format is (or will be in 5.0.0) much faster for these as it includes the 
sequence length and avoids a lot of string copying.

regards,

Peter