I managed to write a program using R to find out all the candidates genes in the database by biomaRt library. I am trying to convert the R script to a python file using rpy2.
Below is the R script written by me that works.
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)
How do I convert the R script above to python script using rpy2?
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)
The error in the last line:
result = R.getBM(attributes = ("hgnc_symbol","entrezgene", "chromosome_name",
"start_position", "end_position") ,filters = ("chromosome_name",
"start", "end", "biotype"), values = filterlist, mart = mart)
States that:
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.
Anyone has any idea how can I convert to python using rpy2 and how can I embed the python code in django so that I can display the data?
As the error says, the Python type tuple
is not converted automatically.
Try the following:
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)
Notes: it would be possible to have a function that guesses what is the intent of the user might, but I consider this the potential source of too many issues. One can customize this by implementing his/her own additional conversion. Alternatively, one can let rpy2 turn a Python list
into an R list and unlist
it.
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)
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