[Bioperl-l] Found bug in fasta.pm

[Aaron J Mackey]

Well if it's going to get stored eventually as a Seq object of one sort or
another, I don't see why this makes any difference ... certainly a string
containing 1Gb of sequence takes less space than an object with a hash
element of 1Gb ...

-Aaron

On Thu, 9 Nov 2000, Matthew Pocock wrote:

> Is reading in LLLLLLarge fasta entries in one lump a good idea?
> 
> Matthew
> 
> Hilmar Lapp wrote:
> 
> > Aaron J Mackey wrote:
> > >
> > > I'm not sure why SeqIO/fasta.pm was migrated to a read-line-by-line
> > > architecture (thus necessitating the nitty-gritty mentioned below), but
> >
> > It wasn't. It reads whole records, at least it tries to, and in the past I
> > advised against suggestions to migrate to line-by-line reading. The winner
> > in your code sample is setting $/ to "\n>" instead of ">" only, and as
> > someone reluctant to delve into those cryptic perl built-in variables ;-) I
> > wasn't aware that you can specify multi-char strings. If no-one else does
> > I'll take care of simplifying the code by exploiting this. The fasta module
> > needs an amendment anyway to correctly cope with empty sequences (which we
> > agreed upon some time ago that we'd like to have it).
> >
> >         Hilmar
> >
> > --
> > -----------------------------------------------------------------
> > Hilmar Lapp                                email: hlapp@gmx.net
> > GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
> > -----------------------------------------------------------------
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> 

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