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Re: st: New program - snpgrab


From   Nick Cox <njcoxstata@gmail.com>
To   statalist@hsphsun2.harvard.edu
Subject   Re: st: New program - snpgrab
Date   Mon, 30 Jan 2012 15:32:53 +0000

For this to work in Stata 10, the -version- statement would need to be
changed and the line

label define Chr_ID_lbl 23 "X" 24 "Y" 25 "MT", replace

would need to be

label define Chr_ID_lbl 23 "X" 24 "Y" 25 "MT", modify

Nick

On Mon, Jan 30, 2012 at 3:16 PM, Elwood Cook <danielecook@gmail.com> wrote:

> Thanks for the feedback.
>
> (1.) This should be able to run under version 11.0, but I am not sure
> about 10 as I am unable to test that.
> (2.) I will create a help file in the next day or two.
> (3.) The data is pulled in using the "efetch" utilities provided by
> pubmed. (http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html)
> (4.) Please feel free to provide more thoughts! If you'd like to try
> it, you could type the following into Stata:
>
>
>
> set obs 100
> gen snp = _n
> snpgrab snp
>
>
>
> I will include more examples in the help file.
>
> I am also working on programs for pulling in data based on gene names,
> ids and publication ID's.
>
> Thanks,
> -E
>
> On Mon, Jan 30, 2012 at 5:30 AM, Tiago V. Pereira
> <tiago.pereira@mbe.bio.br> wrote:
>> I found the idea very interesting. However, I have some remarks:
>>
>> (1) it would be nice to change the version. For example,  version 12.0 to
>> 10.0 (is that possible?)
>> (2) Do you have a help file? I have failed to find it.
>> (3) it is not clear for me where the data come from.
>> (4) I have certainly more observations, but I would need to run it. I
>> manually changed the original code to run -snpgrap- in my Stata 11.0 -
>> unsuccessfully, however. An example would be very helpful.
>>
>> All the best,
>>
>> Tiago
>>
>>
>>
>> ----------------
>> I have written a new program for those in the field of genetics.
>>
>> The program, called snpgrab, will download snp (single nucleotide
>> polymorphism) information when provided with a list of rs numbers.
>> This information includes Gene Name, Gene ID (Entrez), Chromosome,
>> Position (bp), alleles, heterozygosity, and more.
>>
>> Please let me know what you think, and how this can be improved or
>> expanded upon.You can install the program by typing in the following
>> command:
>>
>>
>> net install snpgrab, from(http://www.elwoodcook.com/stata/)
>>
>>
>> To use, enter a list of snp numbers. They can be a string (with the rs
>> prefix) or a numeric variable with the rs left out. Then type:
>>
>> snpgrab rslist
>>
>> where rslist is the variable of a list of snp numbers. (can be string,
>> with rs prefix or numeric without).

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