[R] How do I paste double quotes arround a character string?
Prof Brian Ripley
ripley at stats.ox.ac.uk
Thu Jul 3 15:19:23 CEST 2008
On Thu, 3 Jul 2008, Ted.Harding at manchester.ac.uk wrote:
> I agree with Brian Ripley's suggestions
>
> unix.cmd<-paste( "cut -d -f" , col.pos , " " , fn , sep = '')
> gnu.dat <- read.csv(pipe(unix.cmd))
>
> It is the same conclusion as I came to myself, after reading your
> "correction to small typo" message. In short, no quotes are needed
> by the Unix shell in the command you want it to execute. The
> quotes are only needed to identify, to R, arguments in the paste()
> function as character strings. R then constructs unix.cmd as a
> string, and passes the characters in that string (without bounding
> quotes) as a command line to Unix just as if you had typed it yourself
> at a shell prompt.
>
> On the other hand, if the Unix command itself had needed quotes
> (as in the example ls -l "New Mexico" I used), then you should
> put them in with \". As in (now getting closer to the usage you
> intend):
>
> unix.cmd <- paste("ls -l", "\"New Mexico\"")
Better
unix.cmd <- paste("ls -l", shQuote(New Mexico))
since that will fathom out suitable quotes on the current system, dealing
with embedded quotes.
> unix.cmd
> # [1] "ls -l \"New Mexico\""
> read.table(pipe(unix.cmd))
> # V1 V2 V3 V4 V5 V6 V7 V8 V9
> # 1 -rw-r--r-- 1 ted ted 0 2008-07-03 11:58 New Mexico
>
> which is OK.
>
> By trying to enclose the Unix command itself in quotes, you
> would in effect be giving Unix a command line (including the
> quotes) like:
>
> "ls -l New*"
>
> which has the effect:
>
> ted at deb:~$ "ls -l New*"
> bash: ls -l New*: command not found
>
> In other words, it was looking for a command whose name was,
> literally, 'ls -l New*' and, of course, not finding it.
>
> Hoping things are a bit clearer now!
> Ted.
>
> On 03-Jul-08 11:13:42, Prof Brian Ripley wrote:
>> On Thu, 3 Jul 2008, Philip James Smith wrote:
>>
>>> He Ted:
>>>
>>> My command will look like:
>>>
>>> gnu.dat <- read.csv( pipe( "cut -d,
>>> -f9,2669,2676,2684,506,467,423,6,16,622,474,2,403,19,436,400,444,430,39
>>> 0,2671,437,428,2686,23,21,2246,2326,2288,2282,2272,2360,2318,2262,476,5
>>> 02,605,519,523,527,531,535
>>> /home/philipsmith/file_name.csv" ) )
>>>
>>> This code uses pipe() and the unix command "cut."
>>>
>>> What I'm trying to do is to read certain fields in a .csv file..... my
>>> original .csv file has THOUSANDS of columns, so I just want to read
>>> certain
>>> ones...The unix command "cut" uses -d to specify that the comma ","
>>> is the
>>> delimiter in the file, and the -f to identify the field numbers. After
>>> the
>>> field numbers "cut" wants the file name.
>>>
>>> Evidently, the unix command called by pipe must be within double
>>> quotes...
>>> and that is my problem...
>>
>> That is not 'evident', not even true in your example. You passed
>> pipe() a
>> length-one character vector containing a command, and the quotes were
>> something the parser used to recognize the element of the character
>> vector.
>>
>>>
>>> In my actual problem, I've got THOUSANDS of csv files that contain
>>> some
>>> common variables and other variables that differ from file to file.
>>> I've
>>> specified the variables I want as a character vector called namz, and
>>> read
>>> the first line of each file using scan(). I'm then able to find out
>>> using
>>> match() the positions of the variables I want in each file. the code
>>> listed
>>> above gives only 1 of THOUSANDS of possible configurations of those
>>> desired
>>> variables.
>>>
>>> In order to get this task done, for each file I get the position
>>> numbers in a
>>> variable called "col.pos" and then create the unix command using
>>> paste:
>>>
>>>
>>> unix.cmd <- paste( "cut -d -f" , col.pos , " " , fn , sep = ''
>>> )
>>
>> and then you can use
>>
>> gnu.dat <- read.csv(pipe(unix.cmd))
>>
>> Much simpler!
>>
>>> Then what I want to do is to create the R command that will read the
>>> file...
>>> something like:
>>>
>>>
>>> cmd0 <- paste( "gnu.dat <- read.csv( pipe ( \"" ,
>>> unix.cmd ,
>>> "\" ) ) " , sep='')
>>>
>>>
>>> Then, I'll use
>>>
>>> eval( parse (text = cmd0) )
>>>
>>> to read a file... and embed this in more code to read all of the
>>> THOUSANDS of
>>> files, each 1 at a time.
>>>
>>> However, in the "cmd0" variable, I've used "\"" ... this does not
>>> work... it
>>> yields a character string that looks like...
>>>
>>>
>>>> cmd0
>>> [1] "gnu.dat <- read.csv( pipe ( \"cut -d
>>> -f9,2669,2676,2684,506,467,423,6,16,622,474,2,403,19,436,400,444,430,39
>>> 0,2671,437,428,2686,23,21,2246,2326,2288,2282,2272,2360,2318,2262,476,5
>>> 02,605,519,523,527,531,535
>>> /home/philipsmith/Bubba/NIS/2007_claf/y2007.csv\" ) ) "
>>>>
>>>
>>> You'll see in that line the slash that precedes the double quote. the
>>> pipe()
>>> command is giving unix a unix command that has a slash in it: unix is
>>> expecting only a double quote and not a slash and gives and error.
>>>
>>> So, those are all of the details. I'll be quite grateful if you can
>>> tell me
>>> how to paste a double quote (") in front of and at the end of a string
>>> so
>>> that unix will recognize the string as a valide unix command.
>>
>> Actually, this is a shell command line, which the shell parses and
>> passes
>> to Unix *provided* the parsing is not switched off by quoting.
>>
>> If you want to quote a command string, that is what shQuote() is for.
>>
>>>
>>> Very gratefully,
>>> Phil Smith
>>> Duluth, GA
>>>
>>>
>>>
>>>
>>>
>>>
>>> (Ted Harding) wrote:
>>>> Hi Philip,
>>>> I think a bit more clarification may be useful yet!
>>>>
>>>> 1: How are you sending the command from R to Linux?
>>>> 2: What is the command intended to be (as seen by Linux)?
>>>> And from what source (quasi-command line; script file; ...)
>>>> would it be read by Linux?
>>>>
>>>> For example, on my Linux machine, I just did (in a shell
>>>> command line):
>>>>
>>>> ted at deb:~$ touch "New Mexico"
>>>> ted at deb:~$ ls -l "New Mexico"
>>>> -rw-r--r-- 1 ted ted 0 2008-07-03 10:58 New Mexico
>>>>
>>>> and then, in R, I did:
>>>>
>>>>
>>>>> system("ls -l \"New Mexico\"")
>>>>>
>>>> -rw-r--r-- 1 ted ted 0 2008-07-03 10:58 New Mexico
>>>>
>>>> so I don't seem to have had the problem you describe below.
>>>>
>>>> On the other hand, back in Linux, if I do:
>>>>
>>>> ted at deb:~$ ls -l \"New Mexico\"
>>>> ls: "New: No such file or directory
>>>> ls: Mexico": No such file or directory
>>>>
>>>> which looks like the problem you describe -- so clearly the
>>>> command did not get through in that form from R using the
>>>> command system("ls -l \"New Mexico\"").
>>>>
>>>> Best wishes,
>>>> Ted.
>>>>
>>>> On 03-Jul-08 09:18:14, Philip James Smith wrote:
>>>>
>>>>> Thanks for your reply, Ted... I am very grateful for it.
>>>>>
>>>>> Using your notation, what I need is a character string Y that looks
>>>>> like:
>>>>>
>>>>> >
>>>>> > Y
>>>>> >[1] ""New Mexico""
>>>>>
>>>>> rather than
>>>>>
>>>>> > Y
>>>>> >[1] "\"New Mexico\""
>>>>>
>>>>> i.e., Y must have the string 'New Mexico' surrounded by double
>>>>> quotes,
>>>>> rather than double quotes preceded by slashes.
>>>>>
>>>>> The reason why I need it that way is that I've over simplified my
>>>>> request
>>>>> and the character string is actually a unix command that needs to be
>>>>> surrounded by double quotes when embeded in the unix (linux)
>>>>> executes it.
>>>>> When unix sees that slash before the quotes, it gives an
>>>>> error.
>>>>>
>>>>> I'd be grateful if you can provide a solution to this!!
>>>>>
>>>>> Thank you, Ted!
>>>>>
>>>>> Gratefully,
>>>>> Phil Smith
>>>>> Duluth, GA
>>>>>
>>>>>
>>>>> (Ted Harding) wrote:
>>>>>
>>>>>> On 03-Jul-08 01:25:55, Philip James Smith wrote:
>>>>>>
>>>>>>> Hi R Community:
>>>>>>> I've got a character string that looks like: New Mexico
>>>>>>>
>>>>>>> How to I create the new character string that looks like: "New
>>>>>>> Mexico" That is, it is the original string (New Mexico) with
>>>>>>> double
>>>>>>> quotes infront and behind it?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Phil Smith
>>>>>>>
>>>>>> I tried the following. Is that the sort of thing you want to
>>>>>> achieve?
>>>>>>
>>>>>> X<-"New Mexico"
>>>>>> Y<-"\"New Mexico\""
>>>>>> X
>>>>>> # [1] "New Mexico"
>>>>>> Y
>>>>>> # [1] "\"New Mexico\""
>>>>>> plot((1:10),xlab=X,ylab=Y)
>>>>>>
>>>>>> Best wishes,
>>>>>> Ted.
>>>>>>
>>>>>> --------------------------------------------------------------------
>>>>>> E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
>>>>>> Fax-to-email: +44 (0)870 094 0861
>>>>>> Date: 03-Jul-08 Time:
>>>>>> 09:22:10
>>>>>> ------------------------------ XFMail
>>>>>> ------------------------------
>>>>>>
>>>>>>
>>>>>>
>>>>> ______________________________________________
>>>>> R-help at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide
>>>>> http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>>
>>>> --------------------------------------------------------------------
>>>> E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
>>>> Fax-to-email: +44 (0)870 094 0861
>>>> Date: 03-Jul-08 Time: 11:08:36
>>>> ------------------------------ XFMail ------------------------------
>>>>
>>>>
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>> --
>> Brian D. Ripley, ripley at stats.ox.ac.uk
>> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
>> University of Oxford, Tel: +44 1865 272861 (self)
>> 1 South Parks Road, +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK Fax: +44 1865 272595
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> --------------------------------------------------------------------
> E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
> Fax-to-email: +44 (0)870 094 0861
> Date: 03-Jul-08 Time: 14:03:41
> ------------------------------ XFMail ------------------------------
>
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
More information about the R-help
mailing list