[BioC] Small bug in function 'countskip.FASTA.entries' from package altcdfenvs

[lgautier@altern.org]

> Dear Laurent,
>

<snip>

> Thanks for pointing to these functions! I will give a trail as soon as
> the 'matchprobes' routine is over...
>
> BTW, I launched the script 150 hours ago, but it's still not finished.
> How much computational time should I foresee to need on my standard Mac
> G4 machine (OS X Panther)?
>
> Here are some number to have an idea: I'm
> remapping the MOE430 v2.0 arrays (approximately 1 million probes)
> against roughly 38000 unique EnsEMBL transcripts...

No idea. I just now that it is long.
I remember that the HG-U133A against RefSeq (human-only) took many
days on SGI processors ('don't remember the specs for the processors).
I ended up implementing a drafty way of doing parallel processing (easy to
orthogonalize by dividing the reference sequence in the FASTA file
in chunks). The functions 'skip.FASTA.entries' and 'read.n.FASTA.entries'
were written primarily for that.



Hoping this helps,



Laurent



> Thank you in advance for your feed-back!
>
> Best,
> Norman
>
> Norman Pavelka
> Department of Biotechnology and Bioscience
> University of Milano-Bicocca
> Piazza della Scienza, 2
> 20126 Milan, Italy
>
> Phone: +39 02 6448 3556
> Fax: +39 02 6448 3552
> 	[[alternative text/enriched version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>