[Bioc-sig-seq] limit to character length for read.DNAStringSet()

[Andrew Yee]

Is there a limit to the number of characters in a line for read.DNAStringSet()?

Take for example the following example, which runs fine:

library('Biostrings')

foo <- character()

number.of.characters <- 2000

foo[1] <- '>foo'
foo[2] <- paste(rep('A', number.of.characters), sep='', collapse='')

write(foo, file='~/sandbox/foo.fasta')

bar <- read.DNAStringSet(filepath='~/sandbox/foo.fasta', format='fasta')

# however if I increase number of characters to e.g. 20000, the
example no longer works

foo <- character()

number.of.characters <- 20000

foo[1] <- '>foo'
foo[2] <- paste(rep('A', number.of.characters), sep='', collapse='')

write(foo, file='~/sandbox/foo.fasta')

bar <- read.DNAStringSet(filepath='~/sandbox/foo.fasta', format='fasta')

# the above read.DNAStringSet generates the following error message

> bar <- read.DNAStringSet(filepath='~/sandbox/foo.fasta', format='fasta')
Error in .read.fasta.in.XStringSet(filepath, set.names, elementType, lkup) :
  reading FASTA file     : cannot read line 2, line is too long

Thanks,
Andrew

> sessionInfo()
R version 2.11.1 Patched (2010-09-04 r52880)
Platform: x86_64-unknown-linux-gnu (64-bit)

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_2.16.9 IRanges_1.6.17

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 tools_2.11.1