Passing a Python variable to R using rpy2

Question

I have basic R script that performs a GLM on a MySQL dataset. This runs fine using Rscript in bash. However I would like to call it within a python script so I can add it to a loop, I can create the sql statement but I can't seem to pass it to R using rpy2;

for word in words:
    sql_scores = "select a.article_id, response, score  from scores as a join profile as b on a.article_id = b.article_id where response in (1,0) and keyword = '%s';" % (word[0])
    robjects.r("library(RMySQL)")
    robjects.r("mydb = dbConnect(MySQL(), user='me', password='xxxx', host='aws.host', dbname='mydb')")
    robjects.r("results = fetch(dbSendQuery(mydb, '%s'))") % (sql_scores)
    robjects.r("model <- glm(response ~ score , data=results, family=binomial)")
    robjects.r("summary(model)")

If I print sql_scores I can run this fine directly in MySQL. However Python produces this error;

Loading required package: DBI
Traceback (most recent call last):
  File "keyword_searcher.py", line 30, in <module>
    robjects.r("results = fetch(dbSendQuery(mydb, '%s'))") % (sql_scores)
  File "/usr/local/lib/python2.7/dist-packages/rpy2/robjects/__init__.py", line 268, in __call__
    p = rinterface.parse(string)
 ValueError: Error while parsing the string.

I can't figure out the proper syntax for:

robjects.r("results = fetch(dbSendQuery(mydb, %s))") % (sql_scores)

nick · Accepted Answer · 2018-08-16 18:47:21Z

3

Use double quotes around the "%s" and single quotes around the robjects.r string:

robjects.r('results = fetch(dbSendQuery(mydb, "%s"))') % (sql_scores)

or use the format() method:

robjects.r('fetch(dbSendQuery(mydb, {0}))'.format(sql_scores))

edited Aug 16, 2018 at 18:47

nick

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answered Jun 11, 2015 at 21:01

Meow

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1 Comment

aBiologist Over a year ago

I try using .format like this robjects.r('snvs$LoadFile({})'.format(input_file)) but I get the following error: object 'myresult_file.txt' not found, and when I tried the same approach but not with .format I get no error what do thing is the issue ?

CodePrinz · Accepted Answer · 2020-02-14 09:05:18Z

2

You can access variables in the R environment with robjects.globalenv['varname']. So an alternative way is:

robjects.globalenv['sql_scores'] = sql_scores
robjects.r("results = fetch(dbSendQuery(mydb, sql_scores))")

answered Feb 14, 2020 at 9:05

CodePrinz

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