Added more graphing functionality and basic testing

.gitignore

@@ -9,6 +9,7 @@ __pycache__/
 # Distribution / packaging
 .Python
 env/
+build/
 develop-eggs/
 dist/
 downloads/

README.md

@@ -83,6 +83,14 @@ By default, the output graphs have a DPI of 150. However, the user can change th
 
 	$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta /Users/thisUser/Desktop/DisorderGraphsFolder/ -D 300
 
+**Specify the lines across a graph:**
+``-lines`` / ``--line_intervals``
+
+By default, the graphs have horizontal dashed lines at intervals of 0.2 from 0 to 1. Now, can specify the location of the dashed lines by using the ``-lines`` / ``--line_intervals`` argument
+
+	$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta /Users/thisUser/Desktop/DisorderGraphsFolder/ -lines 0.1 0.2 0.3 0.4 0.5
+
+
 **Remove non-alphabetic characters from file names -**
 By default, the output files contain characters that are non-alphabetic (for example, *predicted_disorder_sp|Q8N6T3|.png*). This is not a problem on some operating systems, but others do not allow files to have names that contain certain characters. To get around this, you can add the ``--remove_characters`` flag. This will remove all non-alphabetic characters from the .fasta header when saving the file. The previous example with the header >sp|Q8N6T3|ARFG1_HUMAN would now save as *predicted_disorder_spQ8N726AR.png*. 
 
@@ -137,6 +145,14 @@ By default, the output graph has a DPI of 150. However, the user can change the
 	meta.graph_disorder("DAPPTSQEHTQAEDKERD", DPI=300)
 
 
+**Specify the lines across a graph -**
+By default, the graphs have horizontal dashed lines at intervals of 0.2 from 0 to 1. Now, can specify the location of the dashed lines by using specifying *line_intervals*
+
+**Example**
+
+	meta.graph_disorder("DAPPTSQEHTQAEDKERD", line_intervals = [0.1, 0.2, 0.3]
+
+
 ### Calculating Percent Disorder
 The ``percent_disorder`` function will return the percent of residues in a sequence that  have predicted consensus disorder values of 50% or more (as a decimal value).
 
@@ -263,6 +279,11 @@ https://github.com/idptools/metapredict/issues
 ### Recent changes
 This section is a log of recent changes with metapredict. My hope is that as I change things, this section can help you figure out why a change was made and if it will break any of your current work flows. The first major changes were made for the 0.56 release, so tracking will start there. Reasons are not provided for bug fixes for because the reason can assumed to be fixing the bug...
 
+#### V0.60
+Change:
+Added functionality to specify the horizontal lines that appear across the graphs rather than only having the option of having the dashed lines appear at intervals of 0.2.
+    This functionality is in both Python and the command line.
+
 #### V0.58
 Change:
 Updated the network with a newly trained network (using the same dataset as the original) that is slightly more accurate.

docs/_build/html/_sources/changes.rst.txt

@@ -5,6 +5,13 @@ About
 ------
 This section is a log of recent changes with metapredict. My hope is that as I change things, this section can help you figure out why a change was made and if it will break any of your current work flows. The first major changes were made for the 0.56 release, so tracking will start there.
 
+V.060
+------
+
+Change:
+Added functionality to specify the horizontal lines that appear across the graphs rather than only having the option of having the dashed lines appear at intervals of 0.2.
+    This functionality is in both Python and the command line.
+
 V0.58
 ------
 

docs/_build/html/_sources/usage/command-line.rst.txt

@@ -72,6 +72,17 @@ By default, the output files have a DPI of 150. However, the user can change the
 	
 	$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta /Users/thisUser/Desktop/DisorderGraphsFolder/ -D 300
 
+
+**Specify the lines across a graph:**
+``-lines`` / ``--line_intervals``
+
+By default, the graphs have horizontal dashed lines at intervals of 0.2 from 0 to 1. Now, can specify the location of the dashed lines by using the ``-lines`` / ``--line_intervals`` argument
+
+.. code-block:: bash
+	
+	$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta /Users/thisUser/Desktop/DisorderGraphsFolder/ -lines 0.1 0.2 0.3 0.4 0.5
+
+
 **Remove non-alphabetic characters from file name:**
 ``--remove_characters``
 

docs/_build/html/_sources/usage/using-in-python.rst.txt

@@ -75,6 +75,18 @@ By default, the output graph has a DPI of 150. However, the user can change the
 	meta.graph_disorder("DAPPTSQEHTQAEDKERD", DPI=300)
 
 
+**Specify the lines across a graph:**
+``-lines`` / ``--line_intervals``
+
+By default, the graphs have horizontal dashed lines at intervals of 0.2 from 0 to 1. Now, can specify the location of the dashed lines by using specifying *line_intervals*
+
+**Example**
+
+.. code-block:: python
+
+	meta.graph_disorder("DAPPTSQEHTQAEDKERD", line_intervals = [0.1, 0.2, 0.3])
+
+
 Calculating Percent Disorder:
 -----------------------------
 

docs/_build/html/changes.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="usage/troubleshooting.html">Metapredict isn’t working!</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Recent changes</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#about">About</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#v-060">V.060</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#v0-58">V0.58</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#v0-57">V0.57</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#v0-56">V0.56</a></li>
@@ -164,6 +165,14 @@ <h1>Recent changes<a class="headerlink" href="#recent-changes" title="Permalink
 <h2>About<a class="headerlink" href="#about" title="Permalink to this headline">¶</a></h2>
 <p>This section is a log of recent changes with metapredict. My hope is that as I change things, this section can help you figure out why a change was made and if it will break any of your current work flows. The first major changes were made for the 0.56 release, so tracking will start there.</p>
 </div>
+<div class="section" id="v-060">
+<h2>V.060<a class="headerlink" href="#v-060" title="Permalink to this headline">¶</a></h2>
+<p>Change:
+Added functionality to specify the horizontal lines that appear across the graphs rather than only having the option of having the dashed lines appear at intervals of 0.2.</p>
+<blockquote>
+<div><p>This functionality is in both Python and the command line.</p>
+</div></blockquote>
+</div>
 <div class="section" id="v0-58">
 <h2>V0.58<a class="headerlink" href="#v0-58" title="Permalink to this headline">¶</a></h2>
 <p>Change:

docs/_build/html/index.html

@@ -194,6 +194,7 @@ <h1>Welcome to metapredict’s documentation!<a class="headerlink" href="#welcom
 </li>
 <li class="toctree-l1"><a class="reference internal" href="changes.html">Recent changes</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="changes.html#about">About</a></li>
+<li class="toctree-l2"><a class="reference internal" href="changes.html#v-060">V.060</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changes.html#v0-58">V0.58</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changes.html#v0-57">V0.57</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changes.html#v0-56">V0.56</a></li>

docs/_build/html/usage/command-line.html

@@ -92,6 +92,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../api.html">Module Documentation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgements.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="troubleshooting.html">Metapredict isn’t working!</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changes.html">Recent changes</a></li>
 </ul>
 
 
@@ -202,6 +203,12 @@ <h2>Graphing Disorder<a class="headerlink" href="#graphing-disorder" title="Perm
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta /Users/thisUser/Desktop/DisorderGraphsFolder/ -D <span class="m">300</span>
 </pre></div>
 </div>
+<p><strong>Specify the lines across a graph:</strong>
+<code class="docutils literal notranslate"><span class="pre">-lines</span></code> / <code class="docutils literal notranslate"><span class="pre">--line_intervals</span></code></p>
+<p>By default, the graphs have horizontal dashed lines at intervals of 0.2 from 0 to 1. Now, can specify the location of the dashed lines by using the <code class="docutils literal notranslate"><span class="pre">-lines</span></code> / <code class="docutils literal notranslate"><span class="pre">--line_intervals</span></code> argument</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta /Users/thisUser/Desktop/DisorderGraphsFolder/ -lines <span class="m">0</span>.1 <span class="m">0</span>.2 <span class="m">0</span>.3 <span class="m">0</span>.4 <span class="m">0</span>.5
+</pre></div>
+</div>
 <p><strong>Remove non-alphabetic characters from file name:</strong>
 <code class="docutils literal notranslate"><span class="pre">--remove_characters</span></code></p>
 <p>By default, the output files contain characters that are non-alphabetic (for example, <em>predicted_disorder_sp|Q8N6T3|.png</em>). This is not a problem on some operating systems, but others do not allow files to have names that contain certain characters. To get around this, you can add the <code class="docutils literal notranslate"><span class="pre">--remove_characters</span></code> flag. This will remove all non-alphabetic characters from the .fasta header when saving the file. The previous example with the header &gt;sp|Q8N6T3|ARFG1_HUMAN would now save as <em>predicted_disorder_spQ8N726AR.png</em>.</p>

docs/_build/html/usage/using-in-python.html

@@ -94,6 +94,8 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../api.html">Module Documentation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgements.html">Acknowledgements</a></li>
+<li class="toctree-l1"><a class="reference internal" href="troubleshooting.html">Metapredict isn’t working!</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changes.html">Recent changes</a></li>
 </ul>
 
 
@@ -206,6 +208,13 @@ <h2>Graphing Disorder<a class="headerlink" href="#graphing-disorder" title="Perm
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">meta</span><span class="o">.</span><span class="n">graph_disorder</span><span class="p">(</span><span class="s2">&quot;DAPPTSQEHTQAEDKERD&quot;</span><span class="p">,</span> <span class="n">DPI</span><span class="o">=</span><span class="mi">300</span><span class="p">)</span>
 </pre></div>
 </div>
+<p><strong>Specify the lines across a graph:</strong>
+<code class="docutils literal notranslate"><span class="pre">-lines</span></code> / <code class="docutils literal notranslate"><span class="pre">--line_intervals</span></code></p>
+<p>By default, the graphs have horizontal dashed lines at intervals of 0.2 from 0 to 1. Now, can specify the location of the dashed lines by using specifying <em>line_intervals</em></p>
+<p><strong>Example</strong></p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">meta</span><span class="o">.</span><span class="n">graph_disorder</span><span class="p">(</span><span class="s2">&quot;DAPPTSQEHTQAEDKERD&quot;</span><span class="p">,</span> <span class="n">line_intervals</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.1</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">])</span>
+</pre></div>
+</div>
 </div>
 <div class="section" id="calculating-percent-disorder">
 <h2>Calculating Percent Disorder:<a class="headerlink" href="#calculating-percent-disorder" title="Permalink to this headline">¶</a></h2>

docs/changes.rst

@@ -5,6 +5,13 @@ About
 ------
 This section is a log of recent changes with metapredict. My hope is that as I change things, this section can help you figure out why a change was made and if it will break any of your current work flows. The first major changes were made for the 0.56 release, so tracking will start there.
 
+V.060
+------
+
+Change:
+Added functionality to specify the horizontal lines that appear across the graphs rather than only having the option of having the dashed lines appear at intervals of 0.2.
+    This functionality is in both Python and the command line.
+
 V0.58
 ------
 

docs/usage/command-line.rst

@@ -72,6 +72,17 @@ By default, the output files have a DPI of 150. However, the user can change the
 	
 	$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta /Users/thisUser/Desktop/DisorderGraphsFolder/ -D 300
 
+
+**Specify the lines across a graph:**
+``-lines`` / ``--line_intervals``
+
+By default, the graphs have horizontal dashed lines at intervals of 0.2 from 0 to 1. Now, can specify the location of the dashed lines by using the ``-lines`` / ``--line_intervals`` argument
+
+.. code-block:: bash
+	
+	$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta /Users/thisUser/Desktop/DisorderGraphsFolder/ -lines 0.1 0.2 0.3 0.4 0.5
+
+
 **Remove non-alphabetic characters from file name:**
 ``--remove_characters``
 

docs/usage/using-in-python.rst

@@ -75,6 +75,18 @@ By default, the output graph has a DPI of 150. However, the user can change the
 	meta.graph_disorder("DAPPTSQEHTQAEDKERD", DPI=300)
 
 
+**Specify the lines across a graph:**
+``-lines`` / ``--line_intervals``
+
+By default, the graphs have horizontal dashed lines at intervals of 0.2 from 0 to 1. Now, can specify the location of the dashed lines by using specifying *line_intervals*
+
+**Example**
+
+.. code-block:: python
+
+	meta.graph_disorder("DAPPTSQEHTQAEDKERD", line_intervals = [0.1, 0.2, 0.3])
+
+
 Calculating Percent Disorder:
 -----------------------------
 

metapredict/backend/meta_graph.py

@@ -12,7 +12,7 @@
 from metapredict.backend import meta_predict_disorder
 from metapredict.backend.meta_predict_disorder import meta_predict as predict
 
-def graph(sequence, name = " ", line_color = "blue", DPI = 150, save_fig = False, output_file = "./predicted_disorder.png"):
+def graph(sequence, name = " ", line_color = "blue", cutoffLines=[], DPI = 150, save_fig = False, output_file = "./predicted_disorder.png"):
 	"""
 	Function for graphing predicted disorder. By default, this function will show a graph.
 	However, if saveFig = True, then it will save the figure (by default) to the location
@@ -70,8 +70,9 @@ def graph(sequence, name = " ", line_color = "blue", DPI = 150, save_fig = False
 	for i in range(0, len(yValues)):
 		disorderValues.append(0.5)
 	axes.plot(xValues, disorderValues, color = "black", linewidth = "1.25")
-	#add dashed lines at 0.2 intervals
-	cutoffLines = [0.2, 0.4, 0.6, 0.8]
+	#add dashed lines at 0.2 intervals if cutoff lines not specified
+	if cutoffLines == []:
+		cutoffLines = [0.2, 0.4, 0.6, 0.8]
 	for i in cutoffLines:
 		tempList = []
 		for j in range(0, len(yValues)):

metapredict/backend/meta_predict_disorder.py

@@ -76,6 +76,7 @@ def meta_predict(sequence, normalized=True, network=brnn_network, device=device,
 	#get output values from the seq_vector based on the network (brnn_network)
 	outputs = network(seq_vector.float()).detach().numpy()[0]
 
+
 	#make empty list to add in outputs
 	output_values = []
 	#for the values 'i' in outputs

metapredict/meta.py

@@ -41,7 +41,7 @@ def predict_disorder(sequence, normalized=True):
     return meta_predict(sequence, normalized=normalized)
 
 
-def graph_disorder(sequence, name = " ", DPI=150):
+def graph_disorder(sequence, line_intervals=[], name = " ", DPI=150):
     """
     Function to plot the disorder of an input sequece. Displays immediately.
 
@@ -54,14 +54,19 @@ def graph_disorder(sequence, name = " ", DPI=150):
     for example set name = "- PAB1", the title on the graph will be "Predicted
     Protein Disorder - PAB1". 
 
+    line_intervals (optional) : List
+        A list of values that you would like to have for lines across the X-axis.
+        The default puts lines at intervals of 0.2.
+            Example: line_intervals = [0.1, 0.2, 0.3, 0.4, 0.5]
+
     DPI (optional) - default value is 150. Increasing this value will increase
     the resolution of the output graph. Decreasing this value will decrease
     the resolution.
     """
     #make all residues upper case 
     sequence=sequence.upper()
     #graph sequence
-    graph(sequence = sequence, name = name, DPI=DPI)
+    graph(sequence = sequence, name = name, cutoffLines=line_intervals, DPI=DPI)
 
 
 
@@ -246,21 +251,28 @@ def predict_disorder_fasta(filepath, save=False, output_path = "", output_name =
             #print IO error
             print("IO error")
 
-def graph_disorder_fasta(filepath, DPI=150, save=True, output_path="", remove_characters=False):
+def graph_disorder_fasta(filepath, DPI=150, line_intervals=[], save=True, output_path="", remove_characters=False):
     """
     Function to make graphs of predicted disorder from the sequences
     in a specified .fasta file. By default will save the generated
     graphs to the location output_path specified in filepath.
     
     Arguments:
     ----------
-    filepath - the path to where the .fasta file is located. The filepath
-    should end in the file name. For example (on MacOS):
-    filepath="/Users/thisUser/Desktop/folder_of_seqs/interesting_proteins.fasta"
+    filepath : String
+        the path to where the .fasta file is located. The filepath
+        should end in the file name. For example (on MacOS):
+        filepath="/Users/thisUser/Desktop/folder_of_seqs/interesting_proteins.fasta"
     
-    DPI (optional) - default value is 150. Increasing this value will increase
-    the resolution of the output graph. Decreasing this value will decrease
-    the resolution. 
+    DPI (optional) : Int
+        default value is 150. Increasing this value will increase
+        the resolution of the output graph. Decreasing this value will decrease
+        the resolution. 
+
+    line_intervals (optional) : List
+        A list of values that you would like to have for lines across the X-axis.
+        The default puts lines at intervals of 0.2.
+            Example: line_intervals = [0.1, 0.2, 0.3, 0.4, 0.5]
 
     save (optional) - by default, the generated graphs are saved. This can be set
     to False, which will result in the graphs being sequentially shown.
@@ -375,8 +387,8 @@ def graph_disorder_fasta(filepath, DPI=150, save=True, output_path="", remove_ch
             #of the fasta header either as is or with characters removed if remove_characters is set to true).
             output = "{}predicted_disorder_{}.png".format(output_path, name)
             #use the graph function (specified in meta_graph from the backend) to save the graph.
-            graph(sequence = sequence, name = title, DPI = DPI, save_fig = True, output_file = output)
+            graph(sequence = sequence, name = title, cutoffLines=line_intervals, DPI = DPI, save_fig = True, output_file = output)
         else:
             #if save was set to False, then just graph the sequences from the .fasta file and show them immediately.
-            graph(sequence = sequence, name = title, DPI = DPI)
+            graph(sequence = sequence, name = title, cutoffLines=line_intervals, DPI = DPI)