Updated for new Django versions and Python3

efm_helper.py

@@ -39,7 +39,7 @@ def run_mummer(fasta_file, org):
         output = subprocess.check_output(['repeat-match', '-n', '16', '-f', fasta_file])
     except:
         raise
-        print "MUMmer command 'repeat-match' failed."
+        print("MUMmer command 'repeat-match' failed.")
     output_lines = output.splitlines()
     # Loop through mummer output and skip the first 2 lines which only contain header information
     for line in output_lines[2:]:
@@ -71,7 +71,7 @@ def run_mummer(fasta_file, org):
     # Initialize list of dictionaries and reformat for tabular output
     output_list = []
     seen = []
-    for repeat_length, location_list in long_repeats.iteritems():
+    for repeat_length, location_list in long_repeats.items():
         for locations in location_list:
             rate_per_repeat = float(0)
             if len(locations) > 2:
@@ -109,7 +109,7 @@ def run_mummer(fasta_file, org):
         output = subprocess.check_output(['show-coords', '-T', '-I 100', '-H', '-d', coords_file.name])
     except:
         raise
-        print "MUMmer command 'nucmer' and 'show-coords' failed."
+        print("MUMmer command 'nucmer' and 'show-coords' failed.")
     finally:
         # Remove the '.delta' file because we're finished with it
         os.remove(coords_file.name)
@@ -196,7 +196,7 @@ def get_repeats_in_window(n, sequence, min_count, org):
 
     # Reformat for tabular output
     output_list = []
-    for index, contents in repeats.iteritems():
+    for index, contents in repeats.items():
         mut_rate = get_mut_rate(contents[1], n, org)
         entry = {'location': [index],
                  'sequence': str(contents[0]),
@@ -438,4 +438,4 @@ def process_efm(form):
             'title': form.cleaned_data['title'],
             'check_features': form.cleaned_data['check_features'],
             'organism': org,
-            'version': EFM_VERSION}
+            'version': EFM_VERSION}

templates/efm/form.html

@@ -5,7 +5,7 @@
 {% if GOOGLE_ANALYTICS_PROPERTY_ID %}
   {% include "efm/ga.html" %}
     {% endif %}
-{% load staticfiles %}
+{% load static %}
 <link href="{% static 'efm/styles.css' %}" rel="stylesheet" type="text/css" media="all" />
     <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.1/jquery.min.js"></script>
     <script type="text/javascript">
@@ -29,7 +29,7 @@ <h1 id="banner"></h1>
 <h3>Please select a file to upload or enter a sequence into the textbox.</h3>
 <p>FASTA, GenBank, or BioBrick XML format files are supported. BioBrick XML files are available from the <a href="http://parts.igem.org/Registry_API" target="_blank">iGEM Registry</a>.</p>
     {{ form.non_field_errors }}
-    <form action="{% url 'efm:index' %}" method="post" enctype="multipart/form-data">
+    <form action="{% url 'index' %}" method="post" enctype="multipart/form-data">
     {% csrf_token %}
         <p><input type="button" id="example" value="Click here for an example sequence" /></p>
     <p>
@@ -61,4 +61,4 @@ <h3>Citing the EFM Calculator</h3>
     <p>Web view powered by Django and SCRIBL.</p>
 </div>
 </body>
-</html>
+</html>

templates/efm/results.html

@@ -5,7 +5,7 @@
            {% if GOOGLE_ANALYTICS_PROPERTY_ID %}
               {% include "efm/ga.html" %}
            {% endif %}
-       {% load staticfiles %}
+       {% load static %}
         <meta charset="utf-8">
         <meta http-equiv="Content-Type" content="text/html">
         <title>EFM Calculator</title>
@@ -173,7 +173,7 @@ <h1 id="banner">Results: {{ title }}</h1>
 			<h2>RIP score: {{ rate.rip|floatformat }}*</h2>
 			<p class="note">*(Lower is more stable.)</p>
             <div id="csv-button">
-				<div><a href="{% url 'efm:index' %}">&larr; New Sequence</a></div>
+				<div><a href="{% url 'index' %}">&larr; New Sequence</a></div>
 				<div><a href="#" class="export">Download CSV</a></div>
                 <div><a href="https://github.com/barricklab/efm-calculator/wiki" target="_blank">Help</a></div>
 			</div>
@@ -198,7 +198,7 @@ <h2>RIP score: {{ rate.rip|floatformat }}*</h2>
                         <td>{{ entry.length.0 }}</td>
                         <td>{{ entry.sequence|default:'&mdash;' }}</td>
                         <td>{{ entry.count }}</td>
-                        <td>{% if entry.type = 'rmd' %}Repeat mediated deletion{% else %}Simple sequence repeat{% endif %}</td>
+                        <td>{% if entry.type == 'rmd' %}Repeat mediated deletion{% else %}Simple sequence repeat{% endif %}</td>
                         <td>{{ entry.raw_rate|stringformat:'.2E' }}</td>
                     </tr>
                     {% endfor %}

urls.py

@@ -1,7 +1,7 @@
-from django.conf.urls import patterns, url
+from django.conf.urls import url
 
 from efm import views
 
-urlpatterns = patterns('',
+urlpatterns = [
     url(r'^$', views.get_sequence, name='index'),
-)
+]

views.py

@@ -9,7 +9,9 @@
 from Bio.SeqRecord import SeqRecord
 from tempfile import NamedTemporaryFile
 import os
-from efm_helper import *
+#from efm_helper import *
+
+from efm.efm_helper import *
 
 # Create your views here.
 class SeqForm(forms.Form):
@@ -27,7 +29,7 @@ class SeqForm(forms.Form):
     check_features = forms.BooleanField(label='Annotated Regions Only', required=False)
     check_features.help_text = 'Only assign rates for hypermutable sites that overlap ' \
                                'with annotated regions. Sequence must be annotated.'
-
+ 
     def clean(self):
         '''
         This is where we detect what type of sequence has been uploaded or placed in in the textbox.
@@ -51,7 +53,7 @@ def clean(self):
                 raise forms.ValidationError('File size is too large.')
         elif sequence:
             with NamedTemporaryFile(delete=False) as data_file:
-                data_file.write(sequence.strip())
+                data_file.write(sequence.strip().encode(encoding='UTF-8'))
 
         del cleaned_data['sequence']
         del cleaned_data['sequence_file']
@@ -153,4 +155,4 @@ def get_sequence(request):
     else:
         form = SeqForm()
 
-    return render(request, 'efm/form.html', {'form': form, 'version': EFM_VERSION})
+    return render(request, 'efm/form.html', {'form': form, 'version': EFM_VERSION})