[R] how to load only lines that start with a particular symbol

[Gabor Grothendieck]

In the Windows cmd shell ^ means escape the next character
so try this (assuming the data you posted
is in genetest.dat in the current directory):

> readLines(pipe("findstr/b ^> genetest.dat"))
[1] ">gene A;....." ">gene B;...."

and on UNIX replace "..." with the corresponding grep command
making sure you appropriately escape the > depending on the
shell you use.

On Tue, Sep 15, 2009 at 4:59 PM, J Chen <jiaxuan.chen at mdc-berlin.de> wrote:
>
> Dear all,
>
> I have DNA sequence data which are fasta-formatted as
>
>>gene A;.....
> AAAAACCCC
> TTTTTGGGG
> CCCTTTTTT
>>gene B;....
> CCCCCAAAA
> GGGGGTTTT
>
> I want to load only the lines that start with ">" where the annotation
> information for the gene is contained. In principle, I can remove the
> sequences before loading or after loading all the lines. I just wonder if
> there's a way to load only lines with a particular pattern. The skip
> argument in read.table() doesn't work for my purpose.
>
> Thanks in advance,
> Jimmy
>
> --
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>
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