needle -filter
David Mathog
mathog at mendel.bio.caltech.edu
Tue Jun 10 15:47:49 UTC 2003
> Peter Rice wrote:
>
> EMBOSS does not (always) read the entire stream - but it would have to
> rewind the input to read a second sequence.
>
> Consider, for example, FASTA format:
>
> >abc
> aaacccgggttt
> >def
> tttgggcccaaa
>
> EMBOSS has to read the first line of the second sequence -
> just to know that the first sequence has ended.
Only the first character of that line, which is what I was
referring to in my earlier post. If the input uses getc()
it can do an ungetc() at the second '>' and then exit.
The next "firstfasta" should pick up the same '>'
as its first character. At least on Unix. ungetc() isn't
the most portable of functions - but all the OS's I know
of allow it to be called at least once. Just don't
expect to be able to call it a thousand times sequentially.
Regards,
David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech
More information about the EMBOSS
mailing list