[EMBOSS] EMBOSS seqret : IntelliGenetics and new DOS lines

[Peter Rice]

Peter C. wrote:
> Hi all,
> 
> I've just updated my Mac to EMBOSS 6.1.0, and have found an
> issue with seqret conversion of IntelliGenetics files. After some
> digging, I think this problem relates to having DOS new lines in
> a file on Unix (in my case, Mac OS X).

we have an application "noreturn" to fix things like this.

If you send me your file I will ty to take a look at whether we shoudl
be catching the funny newline characters.

> P.S. Should I have reported this possible bug via sourceforge?

The emboss-bug at emboss.open-bio.org list is the best way to get our attention

> P.P.S. Back in 2006, I reported a similar issue with a data
> corruption reading stockholm/pfam with DOS newlines
> (Sourceforge Bug #1588956, long since fixed). It seems to
> me that EMBOSS would benefit from explicit testing of all
> the file formats using DOS/Windows newlines when run on
> Unix, and vice versa. Does that sound feasible, or just
> hopelessly ambitious?

We can try ... how well does biopytjhon handle these? (i.e. do we need
such examples for perl, python etc or is this an EMBOSS-specific issue?)

regards,

Peter