Hi,
I have some major performance problems writing fasta files
with Biostrings. I have the full Arabidopsis Chr1 (30MByte) in one DNAString,
and writing that to a file takes ages, as you see from the strace output
below: I obtain ~5 lines (80 chars each) per second. The runtime
of the system call <in brackets> is neglectible.
library(Biostrings)
chromosome <-read.DNAStringSet("Chr1_TAIR9.fasta", "fasta")
write.XStringSet(chromosome, file="/tmp/test.fasta", format="fasta")
Is there a fundamental flaw in my thinking ?
Is there an alternative to write.XStringSet() ?
This happens both on my laptop and a beefy server.
I also tried the (ancient) IRanges_1.0.16 and Biostrings_2.10.22,
and get ~11 lines per second.
Yours,
Steffen
13:06:09.949290 write(4, "TAGGAGTTGATGAAGACATCTAACGAAAATTC"..., 80) = 80 <0.000137>
13:06:10.138835 write(4, "GTGCTCAGGCTTCATTGATAAGGAAAGAAACA"..., 80) = 80 <0.000142>
13:06:10.328395 write(4, "AAAGCAGAAACCGACGTGAAATATTACAGAGA"..., 80) = 80 <0.000133>
13:06:10.537475 write(4, "AGACTACTCGAGAATCATTGCACTGAAGAAAG"..., 80) = 80 <0.000159>
13:06:10.727281 write(4, "AAGTGAAAAGAGAAAGAGAATGTGTGATGTGT"..., 80) = 80 <0.000133>
13:06:10.916854 write(4, "CTTTGCTTTAAATGCAATCAGCTTCACGAGAA"..., 80) = 80 <0.000136>
13:06:11.105687 write(4, "GATTCAAGCTCGTTTCGCTCGCTCCGGGTGAA"..., 80) = 80 <0.000594>
sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biostrings_2.14.12 IRanges_1.4.16
loaded via a namespace (and not attached):
[1] Biobase_2.6.0
--
IPB Halle AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann http://www.IPB-Halle.DE
Weinberg 3 http://msbi.bic-gh.de
06120 Halle Tel. +49 (0) 345 5582 - 1470
+49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409