Initial commit.

Author: afrubin

README.md

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+simdms
+======
+
+simdms is a script for simulating deep mutational scanning data. These datasets are intended to be analyzed using [Enrich2](https://github.com/FowlerLab/Enrich2/). For more information or to cite simdms, please refer to [Enrich2: a statistical framework for analyzing deep mutational scanning data](http://biorxiv.org).
+
+Dependencies
+------------
+
+simdms runs on Python 2.7 and requires the following packages:
+
+* [NumPy](http://www.numpy.org/) version 1.10.4 or higher
+* [SciPy](http://www.scipy.org/) version 0.16.0 or higher
+* [pandas](http://pandas.pydata.org/) version 0.18.0 or higher
+* [PyTables](http://www.pytables.org/) version 3.2.0 or higher
+
+We recommend using a scientific Python distribution such as [Anaconda](https://store.continuum.io/cshop/anaconda/) or [Enthought Canopy](https://www.enthought.com/products/canopy/) to install and manage dependencies. PyTables may not be installed when using the default settings for your distribution. If you encounter errors, check that the `tables` module is present.
+
+To use simdms, git clone or download the repository and run `python simdms.py config.json` from its root directory. simdms takes a json-formatted configuration file as the command line argument.
+
+Questions?
+----------
+
+Please use the [GitHub Issue Tracker](https://github.com/FowlerLab/simdms/issues) to file bug reports or request features.
+
+simdms was written by [Alan F Rubin](mailto:[email protected]) and Hannah Gelman.

config.json

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+{
+  "binding": {
+    "max effect": 1.0,
+    "min effect": 0.05,
+    "sigma": 0.1,
+    "wt effect": 0.5,
+    "wt pctile": 75
+  },
+  "experiment": {
+    "depths": [
+      200
+    ],
+    "replicates": 5,
+    "rounds": 6
+  },
+  "growth": {
+    "max effect": 5.0,
+    "min effect": 0.05,
+    "sigma": 0.1,
+    "wt doublings": 2,
+    "wt effect": 1.0,
+    "wt pctile": 75
+  },
+  "noise": {
+    "jackpot": {
+      "mult high": 50,
+      "mult low": 50,
+      "pct high": 5,
+      "pct low": 5
+    },
+    "reperror": {
+      "freq": 0.1
+    }
+  },
+  "outdir": ".",
+  "population": {
+    "size": 10000000,
+    "starting counts sigma": 0.4,
+    "starting wt freq": 0.01,
+    "variants": 10000
+  }
+}