[Bioperl-l] Found bug in fasta.pm

[Matthew Pocock]

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
>
> --
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> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
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