[bip] welcome!

[Bruce Southey]

Hi,
Thanks for the email as I do agree. What I don't agree with is
sweeping the problem away just because some people are doing it. A
user should not have to find out the hard way what is supported and
what is not.

Regards
Bruce

On 8/2/07, Giovanni Marco Dall'Olio <dalloliogm at gmail.com> wrote:
> Something similar happens for GTF, GFF, and most of the other formats I use.
> People in bioinformatics are used to work with standard formats
> without reading the specifications and changing them as they wish.
>
> This is a great problem: if you want to propose a change in one
> standard format, you have to document it clearly, and also underline
> the changes by declaring a new version, for example 'fasta 1.1'.
>
>
> p.s. we are way off topic, we should not mess in this way with the ml.
> p.p.s.: sorry, I have sent this mail to your address instead of the
> mailing list's one accidentally.
>
>
> 2007/8/1, Brandon King <kingb at caltech.edu>:
> >
> >  The vast majority of applications do not support ';' and if it was a
> > feature of the original format, it has been forgotten and ignored. Making a
> > program support it now would cause more problems than any benefit would
> > provide. If some programs support it and others do not, then we suddenly
> > would have more work to convert the two FASTA formats between each other,
> > and frankly that makes me want to abandon bioinformatics altogether as
> > "standard" file formats has been a huge time sink in the field. FASTA in the
> > form most programs support has been the closest thing to a non-changing file
> > format in bioinformatics, which is sad.
> >
> >  I do understand the desire to make a program as complaint with a particular
> > file format as possible. That is a good thing. In this case, the file format
> > has evolved since the original and has effectively become a de facto
> > standard. I would argue the de facto standard is the right way to go in this
> > case. If you or others disagree, what benefits would it provide vs the
> > amount of extra work and problems it would create?
> >
> >  -Brandon
> >
>
>
> --
> -----------------------------------------------------------
>
> My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com
>
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