minor corrections due to directory changes

RPGroup-PBoC · May 22, 2018 · 6bfa9b9 · 6bfa9b9
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diff --git a/data/sortseq_pymc_dump/20150513_marR_MG1655_LB_na_mut1_4bins_seq.csv.zip b/data/sortseq_pymc_dump/20150513_marR_MG1655_LB_na_mut1_4bins_seq.csv.zip
diff --git a/jupyter_notebooks/SI_B_mutation_diversity.ipynb b/jupyter_notebooks/SI_B_mutation_diversity.ipynb
diff --git a/jupyter_notebooks/SI_B_mutation_histogram.ipynb b/jupyter_notebooks/SI_B_mutation_histogram.ipynb
@@ -33,7 +33,7 @@
     "\n",
     "# Import the project utils\n",
     "import sys\n",
-    "sys.path.insert(0, '../')\n",
+    "sys.path.insert(0, '../code/')\n",
     "import NB_sortseq_utils as utils\n",
     "\n",
     "# Import matplotlib stuff for plotting\n",
@@ -63,13 +63,15 @@
     "mut_region_start = 0\n",
     "mut_region_length = 70\n",
     "\n",
-    "data_fn = '../../data/sortseq_pymc_dump/20150513_marR_MG1655_LB_na_mut1_4bins_seq.csv'"
+    "data_fn = '../data/sortseq_pymc_dump/20150513_marR_MG1655_LB_na_mut1_4bins_seq.csv'"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "#======================================================#\n",

diff --git a/jupyter_notebooks/SI_D_affinity_chromatography_model.ipynb b/jupyter_notebooks/SI_D_affinity_chromatography_model.ipynb
@@ -11,7 +11,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "collapsed": true
    },
@@ -23,12 +23,12 @@
     "import numpy as np\n",
     "\n",
     "# # Import the project utils\n",
-    "# import sys\n",
-    "# sys.path.insert(0, '../')\n",
+    "import sys\n",
+    "sys.path.insert(0, '../code/')\n",
+    "import NB_sortseq_utils as utils\n",
     "\n",
     "# Import matplotlib stuff for plotting\n",
     "import matplotlib.pyplot as plt\n",
-    "import NB_sortseq_utils as utils\n",
     "utils.set_plotting_style1()\n",
     "%matplotlib inline"
    ]

diff --git a/jupyter_notebooks/SI_G_dgoR_simulation.ipynb b/jupyter_notebooks/SI_G_dgoR_simulation.ipynb
@@ -18,7 +18,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "collapsed": true
    },
@@ -33,11 +33,8 @@
     "import matplotlib.pyplot as plt\n",
     "from IPython.core.pylabtools import figsize\n",
     "import sys\n",
-    "sys.path.insert(0, '../')\n",
-    "# sys.path.insert(0, '../../')\n",
-    "# sys.path.insert(0, '../sortseq_pymc/')\n",
+    "sys.path.insert(0, '../code/')\n",
     "import NB_sortseq_utils as utils\n",
-    "# import MCMC_utils\n",
     "\n",
     "# Seaborn, useful for graphics\n",
     "import seaborn as sns\n",

diff --git a/jupyter_notebooks/SI_H_thermodynamic_model_MCMC_processing.ipynb b/jupyter_notebooks/SI_H_thermodynamic_model_MCMC_processing.ipynb
@@ -18,7 +18,9 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "# load in the usual tools\n",
@@ -29,7 +31,7 @@
     "\n",
     "# Import the project utils\n",
     "import sys\n",
-    "sys.path.insert(0, '../')\n",
+    "sys.path.insert(0, '../code/')\n",
     "import NB_sortseq_utils as utils\n",
     "utils.set_plotting_style1()\n",
     "from IPython.core.pylabtools import figsize\n",
@@ -120,6 +122,7 @@
    "cell_type": "code",
    "execution_count": 13,
    "metadata": {
+    "collapsed": true,
     "scrolled": false
    },
    "outputs": [],
@@ -314,7 +317,9 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "# values in MCMC chain (first three are the parameter values that could be fit)\n",
@@ -331,7 +336,9 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "# fig, ax = plt.subplots(len(names),1, figsize=(5,5*len(names)))\n",
@@ -457,14 +464,18 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "code",
    "execution_count": 150,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "# We can also view the distributions using the corner tool\n",

diff --git a/jupyter_notebooks/Sort-Seq_energy_matrix_visualization.ipynb b/jupyter_notebooks/Sort-Seq_energy_matrix_visualization.ipynb
diff --git a/jupyter_notebooks/Sort-Seq_promoter_data_visualization.ipynb b/jupyter_notebooks/Sort-Seq_promoter_data_visualization.ipynb