在Django中使用rpy2和biomaRt

Question

我用R语言写了一个程序，通过biomaRt库找出了数据库中的所有候选基因。现在我想用rpy2把这个R脚本转换成Python文件。

下面是我写的有效的R脚本。

library(biomaRt) 
mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

positions <- read.table("positions.txt")
names(positions) <- c("chr","start","stop")
positions$start <- positions$start - 650000
positions$stop <- positions$stop + 650000

filterlist <- list(positions$chr,positions$start,positions$stop,"protein_coding")

getBM(attributes = c("hgnc_symbol","entrezgene", "chromosome_name", 
"start_position", "end_position"), filters = c("chromosome_name", "start", 
"end", "biotype"), values = filterlist, mart = mart)

我该如何使用rpy2把上面的R脚本转换成Python脚本呢？

from rpy2.robjects import r as R
R.library("biomaRt")
mart = R.useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl")
position = R.list("7","110433484", "110433544")
filterlist = R.list(position[0],position[1],position[2],"protein_coding")

result = R.getBM(attributes = ("hgnc_symbol","entrezgene", "chromosome_name", 
"start_position", "end_position") ,filters = ("chromosome_name", 
"start", "end", "biotype"), values = filterlist, mart = mart)

最后一行的错误信息：

result = R.getBM(attributes = ("hgnc_symbol","entrezgene", "chromosome_name", 
    "start_position", "end_position") ,filters = ("chromosome_name", 
    "start", "end", "biotype"), values = filterlist, mart = mart)

提示内容是：

 Traceback (most recent call last):
  File "<stdin>", line 3, in <module>
  File "/Users/project/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 86, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/Users/project/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 34, in __call__
    new_kwargs[k] = conversion.py2ri(v)
  File "/Users/project/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 148, in default_py2ri
    raise(ValueError("Nothing can be done for the type %s at the moment." %(type(o))))
ValueError: Nothing can be done for the type <type 'tuple'> at the moment.

有没有人知道如何用rpy2转换成Python，并且如何把Python代码嵌入到Django中，以便我可以展示数据呢？

Answer 1

根据错误提示，Python中的类型tuple不会自动转换。

你可以尝试以下方法：

from rpy2.robjects.vectors import StrVector
result = R.getBM(attributes = StrVector(("hgnc_symbol","entrezgene", "chromosome_name", 
                                         "start_position", "end_position")),
                 filters = StrVector(("chromosome_name", 
                                      "start", "end", "biotype")),
                 values = filterlist,
                 mart = mart)

注意：虽然可以创建一个函数来猜测用户的意图，但我认为这样可能会引发很多问题。你可以通过实现自己的额外转换来进行定制。或者，你也可以让rpy2把Python中的list转换成R语言的列表，然后再进行unlist操作。

from rpy2.robjects.packages import importr
base = importr('base')
ul = base.unlist
result = R.getBM(attributes = ul(["hgnc_symbol","entrezgene", "chromosome_name", 
                                  "start_position", "end_position"]),
                 filters = ul(["chromosome_name", 
                               "start", "end", "biotype"]),
                 values = filterlist,
                 mart = mart)