[R] Beginner needs help with R

[Bert Gunter]

Yes, I was replying to the OP's query **as stated.** I try to avoid
guessing what the OP really *meant*, although I grant that sometimes
this may be necessary.

But do note that the leading 0's in seq() *are* unnecessary:

> sprintf("%02d",1:3)
[1] "01" "02" "03"


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 Tue, Feb 7, 2017 at 8:48 AM, Ted Harding <Ted.Harding at wlandres.net> wrote:
> Bert, your solution seems to presuppose that the programmer
> knows beforehand that the leading digit in the number is "0"
> (which in fact is clearly the case in Nabila Arbi's original
> query). However, the sequence might arise from some process
> outside of the progammer's contgrol, and may then either have
> a leading 0 or not.In that case, I think Jim's solution is safer!
> Best wishes,
> Ted.
>
>
> On 07-Feb-2017 16:02:18 Bert Gunter wrote:
>> No need for sprintf(). Simply:
>>
>>> paste0("DQ0",seq.int(60054,60060))
>>
>> [1] "DQ060054" "DQ060055" "DQ060056" "DQ060057" "DQ060058" "DQ060059"
>> [7] "DQ060060"
>>
>>
>> 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, Feb 6, 2017 at 5:45 AM, jim holtman <jholtman at gmail.com> wrote:
>>> You need the leading zeros, and 'numerics' just give the number without
>>> leading zeros.  You can use 'sprintf' for create a character string with
>>> the leading zeros:
>>>
>>>> # this is using 'numeric' and drops leading zeros
>>>>
>>>> seq1 <- paste("DQ", seq(060054, 060060), sep = "")
>>>> seq1
>>> [1] "DQ60054" "DQ60055" "DQ60056" "DQ60057" "DQ60058" "DQ60059" "DQ60060"
>>>>
>>>> # use 'sprintf' to create leading zeros
>>>> seq2 <- paste0("DQ", sprintf("%06d", seq(060054, 060060)))
>>>> seq2
>>> [1] "DQ060054" "DQ060055" "DQ060056" "DQ060057" "DQ060058" "DQ060059"
>>> "DQ060060"
>>>>
>>>
>>>
>>> Jim Holtman
>>> Data Munger Guru
>>>
>>> What is the problem that you are trying to solve?
>>> Tell me what you want to do, not how you want to do it.
>>>
>>> On Sun, Feb 5, 2017 at 8:50 PM, Nabila Arbi <nabilaelarbi1912 at gmail.com>
>>> wrote:
>>>
>>>> Dear R-Help Team!
>>>>
>>>> I have some trouble with R. It's probably nothing big, but I can't find a
>>>> solution.
>>>> My problem is the following:
>>>> I am trying to download some sequences from ncbi using the ape package.
>>>>
>>>> seq1 <- paste("DQ", seq(060054, 060060), sep = "")
>>>>
>>>> sequences <- read.GenBank(seq1,
>>>> seq.names = seq1,
>>>> species.names = TRUE,
>>>> gene.names = FALSE,
>>>> as.character = TRUE)
>>>>
>>>> write.dna(sequences, "mysequences.fas", format = "fasta")
>>>>
>>>> My problem is, that R doesn't take the whole sequence number as "060054"
>>>> but it puts it as DQ60054 (missing the zero in the beginning, which is
>>>> essential).
>>>>
>>>> Could please tell me, how I can get R to accepting the zero in the
>>>> beginning of the accession number?
>>>>
>>>> Thank you very much in advance and all the best!
>>>>
>>>> Nabila
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>> 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.
>>>>
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> 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.
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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 wlandres.net>
> Date: 07-Feb-2017  Time: 16:48:41
> This message was sent by XFMail
> -------------------------------------------------