From: Endre Bakken Stovner <notifications@github.com>
To: kyleam/snakemake-mode <snakemake-mode@noreply.github.com>
Subject: Support R syntax highlighting in R("""-blocks (#6)
Date: Wed, 13 Apr 2016 02:03:33 -0700 [thread overview]
Message-ID: <kyleam/snakemake-mode/pull/6@github.com> (raw)
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Uses purcells robust mmm-library: https://github.com/purcell/mmm-mode
Can be further updated to recognize other strings as embedded R. The template should be easy to follow.
I suggest something like `"""[Rr]` for the case where you need to run R-scripts using shell or write them in a variable to print/debug. But I leave it at your discretion.
Use-cases for suggestion above:
```python
command = """#r
library(csaw)
param = readParam(minq=50, restrict=c({chromosomes_as_string}))"""
print(command)
R(command)
```
or
```python
run_voom_script = """#R
library(edgeR)
normfactors = tail(read.table("{input.normalization_file}", row.names=1, header=F), 18)
colnames(normfactors) = c("norm.factors") # need this name for voom to accept the normfactors
df = read.table("{input.infile}")
x = DGEList(counts=df, norm.factors=as.matrix(normfactors))
y = voom(x)
write.table(y$E, "{output.outfile}", sep=" ")
""".format(**locals())
print(run_voom_script)
# Must craete new instance of R-interpreter to avoid clashing library requirements
with open(output.script, "w+") as script_handle:
script_handle.write(run_voom_script)
shell("Rscript {output.script}")
```
You can view, comment on, or merge this pull request online at:
https://github.com/kyleam/snakemake-mode/pull/6
-- Commit Summary --
* Support R syntax highlighting in R("""-blocks
-- File Changes --
M snakemake-mode.el (15)
-- Patch Links --
https://github.com/kyleam/snakemake-mode/pull/6.patch
https://github.com/kyleam/snakemake-mode/pull/6.diff
---
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Reply to this email directly or view it on GitHub:
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next reply other threads:[~2016-04-13 9:03 UTC|newest]
Thread overview: 7+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-04-13 9:03 Endre Bakken Stovner [this message]
2016-04-13 13:26 ` Support R syntax highlighting in R("""-blocks (#6) Endre Bakken Stovner
2016-04-14 5:51 ` Endre Bakken Stovner
2016-04-14 6:09 ` Endre Bakken Stovner
2016-04-17 19:04 ` Endre Bakken Stovner
2016-04-18 4:22 ` Endre Bakken Stovner
2020-04-17 0:01 ` Kyle Meyer
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