[BioC] how to use writeFASTA

[Martin Morgan]

On 11/01/2011 03:49 PM, wang peter wrote:
> i have two ShortRead object and want write them in two files,
> but failed

ShortRead::writeFasta(trinity1, "/tmp/tmp.fa")

also Biostrings::write.XStringSet(sread(trinity1), "/tmp/tmp.fa")

see

>
>> data.class(trinity1)
> [1] "ShortRead"
>> data.class(trinity2)
> [1] "ShortRead"
>> writeFASTA(trinity1, file="trinity1")
> Error in for (rec in x) { : invalid for() loop sequence
>> writeFASTA(trinity2, file="trinity2")
> Error in for (rec in x) { : invalid for() loop sequence
>> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
> locale:
> [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
> [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
> [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
> [4] LC_NUMERIC=C
> [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> base
> other attached packages:
>   [1] ggplot2_0.8.9       proto_0.3-9.2       reshape_0.8.4
> plyr_1.6
>   [5] ShortRead_1.10.4    Rsamtools_1.4.3     lattice_0.19-30
> Biostrings_2.20.4
>   [9] GenomicRanges_1.4.8 IRanges_1.10.6
> loaded via a namespace (and not attached):
> [1] Biobase_2.12.2 hwriter_1.3    tools_2.13.1
>
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>
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