new app gene_table

requirements/base.txt

@@ -1,3 +1,4 @@
+amas==0.2
 biopython==1.65
 Django==1.8.1
 pyprind==2.9.1
@@ -8,4 +9,4 @@ dataset==0.5.6
 pytz==2015.2
 django-debug-toolbar==1.3.0
 django-suit==0.2.13
-git+https://github.com/django-haystack/django-haystack.git@bd60745ce82318b1819768c9a31db0579228654d
+git+https://github.com/django-haystack/django-haystack.git@bd60745ce82318b1819768c9a31db0579228654d

voseq/gene_table/admin.py

@@ -0,0 +1,3 @@
+from django.contrib import admin
+
+# Register your models here.

voseq/gene_table/forms.py

@@ -0,0 +1,5 @@
+from core.forms import BaseDatasetForm
+
+
+class GeneTableForm(BaseDatasetForm):
+    pass

voseq/gene_table/models.py

@@ -0,0 +1,3 @@
+from django.db import models
+
+# Create your models here.

voseq/gene_table/templates/gene_table/index.html

@@ -0,0 +1,71 @@
+{% extends 'public_interface/base.html' %}
+
+
+{% block additional_css %}
+  {% load staticfiles %}
+    <link rel="stylesheet" type="text/css" href="{% static 'css/tooltipster.css' %}" />
+{% endblock additional_css %}
+
+
+{% block content %}
+<div class="explorer-container">
+  <div class="container">
+    <h3>Create gene table:</h3>
+
+    <div class="alert alert-info" role="alert">
+      <b>Select sequences you want for a dataset by entering the voucher codes and gene codes.</b>
+    </div>
+
+    {% if form.non_field_errors %}
+      <div class="alert alert-warning" role="alert">
+        {% for i in form.non_field_errors %}
+          <b>{{ i }}</b>
+        {% endfor %}
+      </div>
+    {% endif %}
+
+
+    <div class="container">
+      <div class="row">
+
+        <div class="col-xs-12 col-sm-12  col-md-11 col-lg-11 ">
+
+        <form action="/create_gene_table/results/" method="post">
+        <div class="panel panel-primary" style="min-width: 790px;">
+          <div class="panel-heading">
+            <h3 class="panel-title"><b>Enter the required info to make yourself a table in MS Excel format</b></h3>
+          </div>
+
+
+        {% csrf_token %}
+
+        <table class="table table-bordered"><!-- big -->
+            <tr>
+                <td>
+
+                  {% include "core/form_taxonset.html" %}
+
+                </td>
+
+                <td>
+                  {% include 'core/form_geneset.html' %}
+                </td>
+
+            </tr>
+        </table><!-- big -->
+
+        </div><!-- panel -->
+
+
+        </form>
+
+
+        </div><!-- col -->
+
+      </div><!-- row -->
+    </div><!-- container -->
+
+
+  </div>
+</div>
+{% endblock content %}

voseq/gene_table/templates/gene_table/results.html

@@ -0,0 +1,94 @@
+{% extends 'public_interface/base.html' %}
+
+
+{% block content %}
+<div class="explorer-container">
+  <div class="container">
+    <h3>Results:</h3>
+
+
+    <div class="container">
+      <div class="row">
+
+        <div class="col-xs-12 col-sm-12  col-md-11 col-lg-11 col-lg-offset-1">
+
+
+        {% if warnings|length > 0 %}
+        <div class="panel panel-warning" style="min-width: 790px;">
+          <div class="panel-heading">
+            <h3 class="panel-title"><b>During the processing of you dataset some issues were raised
+              <span class="badge"><b>{{ warnings|length }}</b></span>
+            </b></h3>
+          </div>
+
+          <ul class="list-group">
+            {% for i in warnings %}
+            <li class="list-group-item">{{ i }}</li>
+            {% endfor %}
+          </ul>
+        </div><!-- panel -->
+        {% endif %}
+
+
+        {% if errors|length > 0 %}
+        <div class="panel panel-danger" style="min-width: 790px;">
+          <div class="panel-heading">
+            <h3 class="panel-title"><b>During the processing of you dataset some errors were found
+              <span class="badge"><b>{{ errors|length }}</b></span>
+              </b></h3>
+          </div>
+
+          <ul class="list-group">
+            {% for i in errors %}
+              <li class="list-group-item">{{ i }}</li>
+            {% endfor %}
+          </ul>
+        </div><!-- panel -->
+        {% endif %}
+
+
+        <div class="panel panel-primary" style="min-width: 790px;">
+          <div class="panel-heading">
+            <h3 class="panel-title"><b>Your dataset file:</b></h3>
+          </div>
+
+          <table class="table table-bordered">
+            <tr>
+              <td>
+                <textarea readonly style="height: 450px;" wrap="off" class="form-control dataset">{{ dataset }}</textarea>
+              </td>
+            </tr>
+          </table>
+
+        </div><!-- panel -->
+
+        <a href="/create_dataset/results/{{ dataset_file }}">
+        <button class="btn btn-info">
+          <i class="fa fa-download"></i>
+          Download dataset file
+        </button></a>
+
+
+          <br />
+          <br />
+
+      {% if charset_block %}
+         <table class="table table-bordered">
+            <tr>
+              <td>
+                <textarea readonly style="height: 150px;" class="form-control" wrap="soft">{{ charset_block }}</textarea>
+              </td>
+            </tr>
+          </table>
+      {% endif %}
+
+
+        </div><!-- col -->
+
+      </div><!-- row -->
+    </div><!-- container -->
+
+
+  </div>
+</div>
+{% endblock content %}

voseq/gene_table/tests.py

@@ -0,0 +1,3 @@
+from django.test import TestCase
+
+# Create your tests here.

voseq/gene_table/urls.py

@@ -0,0 +1,11 @@
+from django.conf.urls import patterns
+from django.conf.urls import url
+
+from . import views
+
+
+urlpatterns = patterns(
+    '',
+    url(r'^/$', views.index, name='index'),
+    url(r'^/results/$', views.results, name='results'),
+)

voseq/gene_table/views.py

@@ -0,0 +1,112 @@
+from collections import OrderedDict
+import os
+import uuid
+
+from django.shortcuts import render
+from amas import AMAS
+
+from .forms import GeneTableForm
+from core.utils import get_version_stats
+from core.utils import get_voucher_codes
+from core.utils import get_gene_codes
+from create_dataset.utils import CreateDataset
+
+
+def index(request):
+    form = GeneTableForm()
+
+    return render(request, 'gene_table/index.html',
+                  {
+                      'form': form,
+                  },
+                  )
+
+
+def results(request):
+    version, stats = get_version_stats()
+    if request.method == 'POST':
+        form = GeneTableForm(request.POST)
+        if form.is_valid():
+            print(">>>>", form.cleaned_data)
+            table = GeneTable(form.cleaned_data)
+            print(table.stats)
+            return render(request, 'gene_table/results.html',
+                          {
+                              'version': version,
+                              'stats': stats,
+                          },
+                          )
+
+
+class GeneTable(object):
+    def __init__(self, cleaned_data):
+        self.cleaned_data = self.populate_cleaned_data_form(cleaned_data)
+        self.voucher_codes = get_voucher_codes(cleaned_data)
+        self.gene_codes = get_gene_codes(cleaned_data)
+        self.fasta_dataset = self.get_fasta_dataset()
+        self.fasta_partitions = self.split_in_partitions()
+        self.stats = self.get_stats_from_partitions()
+
+    def populate_cleaned_data_form(self, cleaned_data):
+        cleaned_data['number_genes'] = None
+        cleaned_data['aminoacids'] = False
+        cleaned_data['positions'] = ['ALL']
+        cleaned_data['file_format'] = 'FASTA'
+        cleaned_data['partition_by_positions'] = 'ONE'
+        cleaned_data['taxon_names'] = ['CODE', 'GENUS', 'SPECIES']
+        cleaned_data['outgroup'] = ''
+        return cleaned_data
+
+    def get_fasta_dataset(self):
+        fasta = CreateDataset(self.cleaned_data)
+        return fasta.dataset_str
+
+    def split_in_partitions(self):
+        partitions = OrderedDict()
+
+        lines = self.fasta_dataset.split('\n')
+        for line in lines:
+            this_line = line.replace('>', '')
+            if this_line in self.gene_codes:
+                this_gene = this_line
+                partitions[this_gene] = ''
+            elif this_line.startswith('---------------'):
+                continue
+            else:
+                partitions[this_gene] += line + '\n'
+
+        return partitions
+
+    def get_stats_from_partitions(self):
+        """These are the stats headers of AMAS v0.2
+
+        dna_header = [
+            "Alignment_name",
+            "No_of_taxa",
+            "Alignment_length",
+            "Total_matrix_cells",
+            "Undetermined_characters",
+            "Missing_percent",
+            "No_variable_sites",
+            "Proportion_variable_sites",
+            "Parsimony_informative_sites",
+            "Proportion_parsimony_informative",
+        ]
+        """
+        in_file = self.make_guid() + '.fas'
+
+        for code, partition in self.fasta_partitions.items():
+            with open(in_file, 'w') as handle:
+                handle.write(partition)
+
+            aln = AMAS.DNAAlignment(in_file, 'fasta', 'dna')
+            print(aln.summarize_alignment())
+            print(code, partition)
+
+        try:
+            os.remove(in_file)
+        except OSError:
+            pass
+
+    def make_guid(self):
+        return uuid.uuid4().hex

voseq/public_interface/templates/public_interface/base.html

@@ -105,6 +105,7 @@
                   <li><a href="/blast_new/">Blast new sequence</a></li>
                   <li><a href="/genes/">View genes</a></li>
                   <li><a href="/create_dataset/">Create new dataset</a></li>
+                  <li><a href="/create_gene_table/">Create Gene table</a></li>
                   <li><a href="/genbank_fasta/">Create GenBank FASTA file</a></li>
                 </ul>
               </div>

voseq/public_interface/templates/public_interface/toolbox.html

@@ -4,5 +4,6 @@ <h2>Tools:</h2>
   <li><a href="/blast_new/">Blast new sequence</a></li>
   <li><a href="/genes/">View genes</a></li>
   <li><a href="/create_dataset/">Create new dataset</a></li>
+  <li><a href="/create_gene_table/">Create Gene table</a></li>
   <li><a href="/genbank_fasta/">Create Genbank FASTA file</a></li>
 </ul>

voseq/voseq/settings/base.py

@@ -48,6 +48,7 @@
     'stats',
     'view_genes',
     'genbank_fasta',
+    'gene_table',
 )
 
 MIDDLEWARE_CLASSES = (

voseq/voseq/urls.py

@@ -3,6 +3,7 @@
 
 urlpatterns = patterns(
     '',
+    url(r'^create_gene_table', include('gene_table.urls', namespace='gene_table')),
     url(r'^create_dataset', include('create_dataset.urls', namespace='create_dataset')),
     url(r'^genbank_fasta', include('genbank_fasta.urls', namespace='genbank_fasta')),
     url(r'^blast_local', include('blast_local.urls', namespace='blast_local')),
@@ -11,6 +12,6 @@
     url(r'^blast_new', include('blast_new.urls', namespace='blast_new')),
     url(r'^genes', include('view_genes.urls', namespace='view_genes')),
     url(r'^', include('public_interface.urls', namespace='public_interace')),
-    
+
     url(r'^admin/', include(admin.site.urls)),
 )