Quick example generating a fasta file that does not contain newlines to
illustrate;

library(Biostrings)

set.seed(42)
n   <- 20000
dna <- paste(sample(c("A","T","G","C"), n, replace=TRUE), collapse="")

## Create a fasta file that does not contain newlines
write(">test sequence", "test.fasta")
write(dna, "test.fasta", append=TRUE)

## n=20,000 bases or above will fail
try(read.DNAStringSet("test.fasta"))
Error in .Call2("read_fasta_in_XStringSet", efp_list, nrec, skip,
use.names,  :
  reading FASTA file test.fasta: cannot read line 2, line is too long

n   <- 20000-1
dna <- paste(sample(c("A","T","G","C"), n, replace=TRUE), collapse="")

write(">test sequence", "test.fasta")
write(dna, "test.fasta", append=TRUE)

## 19999 bases or less will load
read.DNAStringSet("test.fasta")
  A DNAStringSet instance of length 1
    width seq
names
[1] 19999 GCTCCTTGGACCGCTCACTGCTC...TTAGATTCACCTTGGCATGAAGT test sequence

Marcus


 sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New
Zealand.1252
[3] LC_MONETARY=English_New Zealand.1252
LC_NUMERIC=C
[5] LC_TIME=English_New Zealand.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] ShortRead_1.12.4    latticeExtra_0.6-19 RColorBrewer_1.0-5
 [4] Rsamtools_1.6.3     Biostrings_2.22.0   GenomicRanges_1.6.7
 [7] IRanges_1.12.6      nlme_3.1-103        NGS_0.9.4
[10] lattice_0.20-6

loaded via a namespace (and not attached):
 [1] Biobase_2.14.0     bitops_1.0-4.1     BSgenome_1.22.0
grid_2.14.1
 [5] hwriter_1.3        RCurl_1.91-1.1     rtracklayer_1.14.4
tools_2.14.1
 [9] XML_3.9-4.1        zlibbioc_1.0.1

On Tue, Apr 10, 2012 at 6:17 AM, Marcus Davy <mdavy86@gmail.com> wrote:

> Sounds like you have Fasta files which do not contain newlines, use the
> linux command 'fold'
> to fix this.
>
> fold [malformedFile] > [newFile]
>
> From memory, read.DNAStringSet() will fail if the file is larger than
> 20,000 characters
> and contains no newline feeds.
>
> Marcus
>
>
> On Tue, Apr 10, 2012 at 12:50 AM, wang peter <wng.peter@gmail.com> wrote:
>
>> hi all
>> sorry to disturb you
>>
>> i forgot how to deal with too long fasta sequences ？
>> i remembered a person told me to use linux command line?
>>
>> thank you in advances
>>
>> --
>> shan gao
>> Room 231(Dr.Fei lab)
>> Boyce Thompson Institute
>> Cornell University
>> Tower Road, Ithaca, NY 14853-1801
>> Office phone: 1-607-254-1267(day)
>> Official email:sg839@cornell.edu
>> Facebook:http://www.facebook.com/profile.php?id=100001986532253too long
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
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>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>

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