[Bioperl-l] Bio::Tools::Glimmer

Mark Johnson johnsonm at gmail.com
Wed Feb 7 11:50:05 EST 2007


    Well, each format has some unique features.  If the user declines to
specify the format, I can figure it out, but it will probably involve
scanning the input file twice.  I'll take a look.
    I can do all the parsing in one function, in fact I have, just to see
how nasty it would end up being.  I just can't stomach having the code that
tightly coupled and hard to read.  In the end it'll probably be three
functions.  GlimmermM/HMM are pretty close.  Maybe two, Glimmer2 and
Glimmer3 aren't *that* different, either.

On 2/6/07, Jason Stajich <jason at bioperl.org> wrote:
>
> I definitely vote for 1) - worst case you have 4 separate methods if there
> is no good way to condense the parsing for each format and require the user
> to specify the format.
>
> I have no problem with requiring user to specify what program she used -
> if we can be fancy and guess the format later (i.e. guess format in SeqIO)
> -then that's icing.
>
> -jason
>
>


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