[BioC] writing a fasta file in blocks

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Wed Jun 9 02:31:34 CEST 2010

Doing what Fahim suggests internally in writeFASTA has been on my todo
list for a while, and it will significantly speed up the writing of
fasta files with many small records.  Guess I should do it now, and
cross it off my list.

But Fahim: I am not sure it is possible to do what you want to do with
the current function (at least if you are using Biostrings), but I
could be wrong.  If you want to investigate further, note that the
file can be a connection (?connection).


On Tue, Jun 8, 2010 at 4:26 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Mon, Jun 7, 2010 at 11:12 PM, Fahim Md <fahim.md at gmail.com> wrote:
>> I have a data File, the format of which is given below. It has two fields,
>> namely  sequence and probeset name.
>>    sequence                                       Probe Set Name
>> ............
>> Now, I want to convert that into FASTA format as follows
>> >1367452_at.1
>> >1367452_at.2
>> >1367452_at.3
>> .......
>> ....
>> >1234567_at.1
>> I am getting the required output by using writeFASTA(..) function but it is
>> too slow because I am using loop and in every loop it access the file to
>> write into.
>> Is there anyway through which I can write this fasta information into some
>> variable and once I am done I write back that  variable into the required
>> file.
> Hi,Fahim.
> Probably most appropriate for here and not bioc-devel.  Perhaps a
> reproducible code example and some sessionInfo() would be helpful.
> Sean
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