I know that we could use markdown for the compilation of documents within Rstudio. We could use it for shell programming, python, perl, R, etc.
My question is:
I have python code, that will generate a table for the input file. Please also tell me, how can I import python packages (while generating the markdown documentation) that are not within python and need to be downloaded and installed separately. I tried to import the tabulate package here, but I was not able to do that. Here is the markdown format:
from sys import argv
file = open("DAS217.txt", 'r')
mydict = {}
for line in file.readlines():
if (line[0] != '#'):
mylist = line.rstrip().split()
if (len(mylist) < 4):
continue
key = mylist[2]
value = mylist[3]
if (mydict.has_key(key) == False):
mydict[key] = [value]
else:
mydict[key].append(value)
from tabulate import tabulate
table<- tabulate({"synonymous_variant":mydict["synonymous_variant"],"missense_variant": mydict["missense_variant"]}, headers="keys")
</pre>
What I want is, to import the "table" object in the R in a single markdown documentation:
tab<- data.frame(table)
head(tab)
Basic idea is: use multiple programming languages and compile one document out of it and importing the output of one to another, within one markdown script. I want to compile this pdf. Is it possible?
