I am a biologist trying to run a particular script (http://www.ricediversity.org/tools/code/Plumage%20Script%202%20F2%20Populations.zip) on my data-set. I have installed python 3.4, panda 0.14.0 and numpy dependecies on my windows 7 laptop as the instructions demand. My data set is in excel file. How do I go forth applying this script to my data? I have no experience with python scripts/ program.
Thank you for your time.
python Plumage2_for_F2.py -h
should give you the usage information. (Being on Windows, simply invoking as Plumage2_for_F2.py does not work as it would on a Unixoid system, so be sure to preface all your commands with python, as above.) The file (as supplied by the -i option) will have to be a CSV (comma-separated values), which you can export from Excel (I do not know the current version of Excel, but it should be something like Save As, or Export).
Related
I want to run an R command from command line (actually, from within a Makefile). The command is roxygen2::roxygenise(), if it is relevant. I don't want to create a new file and run that as a script - that will just clutter my directory.
In python, this is simple - you write python -c "import antigravity".
I use the Makefile to build, install and test a (Rcpp) package I'm working on.
This is generally done with so 'shebang scripts'.
Historically, littler was there first, about a decade or so ago. It is still widely used, and contains a number of helper scripts as for example roxy.r which does just what you desire: run roxygen2::roxygenize(). I use this all the time.
Next, Rscript started to ship with R. It is similar to littler but automatically available whereever R is which is a plus. On the minus side, it starts slower, and fails to load the methods package which is a source of a number of bug reports and SO questions.
Much more recently, R itself added the ability to run expressions following the -e ... switch.
So you have plenty of choices. You can also study plenty of src/Makevars files many of which use Rscript.
I have this very basic piece of Python which I use to visualize some data and perform a few interactions with. I launch it from Spyder and it is basically just a function.
In broad terms:
open a file and create a DataFrame from it
plot some data and add a few sliders to interact with the data
I was wondering whether I could make this small code available to other people who do not have Python installed and probably not even the latest Qt5 libs I am using.
Os would be Linux but could also be Windows if it came easier.
Can you tell me how time consuming would it be to create a standalone file which could be double clicked and just show the plot with the interactive bits?
Just followed the (2 line!) instructions on PyInstaller:
$ echo "print 'hello world...'" > helloworld.py
$ pip install pyinstaller
$ pyinstaller helloworld.py
$ dist/helloworld/helloworld
hello world...
Looks pretty automated. It analyses your dependencies as far I can tell and brings everything you need together and then makes a launch script. It works on loads of platforms and even mentions Qt on the front page. I reckon its worth a go!
I've just had RStudio crash on me unexpectedly, and on re-starting, contrary to what I've come to expect, the R script I had been tinkering around with was nowhere to be found.
I've managed to track down the Rhistory file so I'll be able to piece together all the commands, which is reassuring.
However, I am curious if there's somewhere I might try looking to find the temporary unsaved file on the off chance that might be cached somewhere (after all, it is usually cached somewhere that RStudio apparently knows to look). Is there a particular file extension/format I should be searching for?
Currently running R 3.3.1 through RStudio 0.99.903 on Linux Mint 17.3 (over Ubuntu 14.04.3 LTS).
I've tried running grep on the command line to find some of the more recently updated lines of code; I may be out of luck. I found two files:
~/.rstudio-desktop/history_database
Which appears to basically be a more centralized .Rhistory for RStudio
and
~/.rstudio-desktop/sdb/s-9CD2C698/D7986B2A
This looks JSON-like and also appears to basically be an Rhistory. Please correct me if I'm wrong.
As indicated by #KevinUshey from RStudio:
RStudio stores autosave data as part of the JSON 'blobs' within the sdb folder. You should see the document serialized as a long 'string', with newlines embedded.
Use packages such as jsonlite to parse this and best of luck.
if you used Rstudio on linux, the temporary R script files were stored in .rstudio/sources folder, and you can open all of the script files directly.
Good luck
In Rstudio if you saved or not a script but you ran this code, you can check the history off the app, this is the "telemetric data" that Rstudio has about you.
In windows, this is the path,
C:\Users\ANALISTA\AppData\Local\RStudio\history_database
you should use "visual studio code" or something similar to see it.
Hej,
When I try to call QIIME with a system call from R, i.e
system2("macqiime")
R stops responding. It's no problem with other command line programs though.
can certain programs not be called from R via system2() ?
MacQIIME version:
MacQIIME 1.8.0-20140103
Sourcing MacQIIME environment variables...
This is the same as a normal terminal shell, except your default
python is DIFFERENT (/macqiime/bin/python) and there are other new
QIIME-related things in your PATH.
(note that I am primarily interested to call QIIME from R Markdown with engine = "sh" which fails, too. But I strongly suspect the problems are related)
In my experience, when you call Qiime from unix command line, it usually creates a virtual shell of it`s own to run its commands which is different from regular system commands like ls or mv. I suspect you may not be able to run Qiime from within R unless you emulate that same shell or configuration Qiime requires. I tried to run it from a python script and was not successful.
I am a newbie to UNIX, i want to print tree structure of files in a directory. below image is example in DOS, what will be the command of Unix to achieve same objective
I think you are looking for the "tree" command. If you are having issues running it you might have to find out how to install it on your specific distribution. For ubuntu installs you can find instructions here:
https://askubuntu.com/questions/507588/not-able-to-install-tree-comand-in-ubuntu
Not sure what you mean by "on Unix". What OS are you running, specifically? Tree should be compatible on Unix systems. You may just have to compile it for your particular OS.
This command prints output like the following (on cygwin):