[bip] welcome!

[Giovanni Marco Dall'Olio]

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
>


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My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com