links to docs

README.md

@@ -1,6 +1,10 @@
 
 #Python API for analyzing and manipulating genotype-phenotype maps
 
+
+[![Join the chat at https://gitter.im/harmslab/gpmap](https://badges.gitter.im/harmslab/gpmap.svg)](https://gitter.im/harmslab/gpmap?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Documentation Status](https://readthedocs.org/projects/gpmap/badge/?version=latest)](http://gpmap.readthedocs.io/en/latest/?badge=latest)
+
 This package defines a standard data-structure for genotype-phenotype (GP) map data.
 Useful for creating network graphs (via NetworkX) from GP data. Subset, manipulate,
 extend, etc. GP maps. Calculate statistics, model evolutionary trajectories, predict

docs/_pages/gpm.rst

@@ -1,7 +1,7 @@
 GenotypePhenotypeMap
 ====================
 
-The ``GenotypePhenotypeMap`` class is the primary tool provided by the ``seqspace`` package.
+The ``GenotypePhenotypeMap`` class is the primary tool provided by the ``gpmap`` package.
 It creates intuitive and useful mapping on the fly. It appends methods and attributes
 to make analyzing genotype-phenotype data easy. We've create other packages that
 easily interact with the ``GenotypePhenotypeMap``.

docs/_pages/tutorials.rst

@@ -10,7 +10,7 @@ To begin using this package, import the base class of the package, `GenotypePhen
 
 .. code-block:: python
 
-    import GenotypePhenotypeMap
+    from gpmap import GenotypePhenotypeMap
 
 There a few ways you initialize a GenotypePhenotypeMap object. First, you can pass
 the data into the object directly:

gpmap/simulate/base.py

@@ -1,5 +1,7 @@
 import random
+import numpy as np
 from gpmap import utils
+from gpmap.gpm import GenotypePhenotypeMap
 
 def random_mutation_set(length, alphabet_size=2):
     """Generate a random mutations dictionary for simulations.
@@ -20,3 +22,43 @@ def random_mutation_set(length, alphabet_size=2):
     alphabet = utils.AMINO_ACIDS[:size]
     mutations = dict([(i, alphabet[i])for i in range(length)])
     return mutations
+
+class GenotypePhenotypeSimulation(GenotypePhenotypeMap):
+    """ Build a simulated GenotypePhenotypeMap. Generates random phenotypes.
+    """
+    def __init__(self, wildtype, mutations, range=(0,1), *args, **kwargs):
+        # build genotypes
+        genotypes = utils.mutations_to_genotypes(wildtype, mutations)
+        phenotypes = np.empty(len(genotypes), dtype=float)
+        super(GenotypePhenotypeSimulation, self).__init__(wildtype, genotypes,
+            phenotypes,
+            *args,
+            **kwargs,
+        )
+        self.set_random(range=range)
+
+    def set_random(self, range=(0,1)):
+        """ Get a set of random
+        """
+        self.phenotypes = np.random.random(range[0], range[1], size=self.n)
+
+    @classmethod
+    def from_length(cls, length, alphabet_size=2, *args, **kwargs):
+        """ Create a simulate genotype-phenotype map from a given genotype length.
+
+        Parameters
+        ----------
+        length : int
+            length of genotypes
+        alphabet_size : int (optional)
+            alphabet size
+
+
+        Returns
+        -------
+        self : GenotypePhenotypeSimulation
+        """
+        mutations = random_mutations_set(lengths, alphabet_size=alphabet_size)
+        wildtype = ".join"([m[0] for m in mutations.values()])
+        self = cls(wildtype, mutations, *args, **kwargs)
+        return self