Re: [R] Memory leak with character arrays?

From: Jean lobry <lobry_at_biomserv.univ-lyon1.fr>
Date: Thu 18 Jan 2007 - 13:00:17 GMT

Dear Peter,

>The file that I'm reading contains the upstream regions of the yeast
>genome, with each upstream region labeled using a FASTA header, i.e.:
>
> FASTA header for gene 1
> upstream region.....
> .....
> ....
> FASTA header for gene 2
> upstream....
> ....

you may want to have a look at the read.fasta() function in the seqinr package. There is an example page 16 of this document: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-6.pdf about importing the content of a fasta file with 21,161 sequences from Arabidopsis thaliana into an object which is about 15 Mb in RAM.

HTH,

-- 
Jean R. Lobry            (lobry@biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo  : +33 472 43 27 56     fax    : +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/

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Received on Fri Jan 19 00:16:37 2007

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