[Bioperl-l] Re: GuessSeqFormat problems

[Albert Vilella]

El dl 15 de 08 del 2005 a les 18:11 -0400, en/na Jason Stajich va
escriure:
> 
> 
> Albert - 
> 
> 
> I think the new guessing changes for phylip are causing havoc.   Lots
> of tests are failing t/GuessSeqFeature.t.  Can you take a look?

Uops, sorry about that.

I was trying to make the match for phylip more generic in $lineno=2. In
my case it was returning an unexistent Bio::AlignIO::pir.

I have fixed it and now passes all the tests.

> 
> 
> I was looking over this module - it seems like we probably want to run
> the tests in a particular order as some matches are ambiguous and we
> probably need to have preferred order. At least we'll know when
> something fails, what the order.

As I understand from the DESCRIPTION, the more lines one checks, the
better is determined, isn't it?

Maybe it would help to add more line checks in some of the formats, that
are loosely constricted in their first lines.


> Another thing is it uses open directly instead of allowing Root::IO to
> open a filehandle.  If went to using Root::IO, it would allow peeking
> at not only a file but a filehandle/stream and then use _pushback
> after we have peeked over the first few lines, guess the format, then
> pass it along to the SeqIO/AlignIO handle appropriately.
> 
> 
> Anyways, just thoughts...
> 
> 
> -jason
> --
> 
> Jason Stajich
> 
> jason.stajich at duke.edu
> 
> http://www.duke.edu/~jes12/
> 
> 
> 
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