lines those not started with "rs"

Hi all;

I have a file which has about 3.000.000 lines. Most of the lines at first
column start with "rs", for example, rs10000056, rs10000076 and so on. I
would like to get the lines which do not start with "rs" . Your helps
highly appreciated.

Regards,

Greg

	[[alternative HTML version deleted]]

Greg,

I am assuming that your data is in a text file. R is a good tool but not
the tool I would use for this job. The tool I would
use is grep. The following command should get you want you want:
         grep -v "^rs" <data file name>

Bob


On 1/30/2017 9:23 AM, greg holly wrote:

Hi all;

I have a file which has about 3.000.000 lines. Most of the lines at first
column start with "rs", for example, rs10000056, rs10000076 and so on. I
would like to get the lines which do not start with "rs" . Your helps
highly appreciated.

Regards,

Greg

        [[alternative HTML version deleted]]

Hi Robert;

I do appreciate your advice. Only the first column of the data is 
text. The rest columns are numeric.

Regards,

Greg

On Mon, Jan 30, 2017 at 9:36 AM, Robert Sherry <rsherry8 at comcast.net 
<mailto:rsherry8 at comcast.net>> wrote:

    Greg,

    I am assuming that your data is in a text file. R is a good tool
    but not the tool I would use for this job. The tool I would
    use is grep. The following command should get you want you want:
             grep -v "^rs" <data file name>

    Bob


    On 1/30/2017 9:23 AM, greg holly wrote:

        Hi all;

        I have a file which has about 3.000.000 lines. Most of the
        lines at first
        column start with "rs", for example, rs10000056, rs10000076
        and so on. I
        would like to get the lines which do not start with "rs" .
        Your helps
        highly appreciated.

        Regards,

        Greg

                [[alternative HTML version deleted]]

Hi all;

I have a file which has about 3.000.000 lines. Most of the lines at first
column start with "rs", for example, rs10000056, rs10000076 and so on. I
would like to get the lines which do not start with "rs" . Your helps
highly appreciated.

Regards,

Greg

	[[alternative HTML version deleted]]

Hello,

Try to study the following example.

A <- c("rs10000056", "rs10000076", "ab1234567")
x <- 1:3
dat <- data.frame(A, x)

inx <- grepl("^rs", dat$A)
dat[!inx, ]


Hope this helps,

Rui Barradas

Em 30-01-2017 14:23, greg holly escreveu:

Hi all;

I have a file which has about 3.000.000 lines. Most of the lines at first
column start with "rs", for example, rs10000056, rs10000076 and so on. I
would like to get the lines which do not start with "rs" . Your helps
highly appreciated.

Regards,

Greg

        [[alternative HTML version deleted]]

Rui, et. al.:

**IF** the data set can be read into R (3e6 lines x ?bytes/line ??) ,
then I think for a completely specified regular pattern such as that
described by the OP, grep would be a bit inefficient. If x is a vector
of strings, and you wish to remove all those that don't begin with
"rs" then:

 x[!substring(x,1,2) == "rs"]

took about 1/2 the time on my computer as the grepl() version for a
vector,x, of length 1e6.

To be fair, I suspect this may be a negigible difference, as most of
the time would probably be taken in extracting and replacing rows from
the data frame. Nevertheless, it seems worthwhile to highlight the use
of simple, efficient, albeit limited, tools when they *can* be used.

All, of course, assuming I have understood the query correctly.

Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, Jan 30, 2017 at 8:59 AM, Rui Barradas <ruipbarradas at sapo.pt> wrote:

Hello,

Try to study the following example.

A <- c("rs10000056", "rs10000076", "ab1234567")
x <- 1:3
dat <- data.frame(A, x)

inx <- grepl("^rs", dat$A)
dat[!inx, ]


Hope this helps,

Rui Barradas

Em 30-01-2017 14:23, greg holly escreveu:

Hi all;

I have a file which has about 3.000.000 lines. Most of the lines at first
column start with "rs", for example, rs10000056, rs10000076 and so on. I
would like to get the lines which do not start with "rs" . Your helps
highly appreciated.

Regards,

Greg

        [[alternative HTML version deleted]]