5 files changed, 259 insertions, 0 deletions
diff --git a/CRESSdna.html b/CRESSdna.html
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--- /dev/null
+++ b/CRESSdna.html
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+<!DOCTYPE html>
+
+<html>
+<head>
+<style>
+* {box-sizing: border-box}
+body {font-family: "Lato", sans-serif;}
+
+/* Style the tab */
+div.tab {
+    float: left;
+    border: 1px solid #ccc;
+    background-color: #f1f1f1;
+    width: 20%;
+    height: 250px;
+}
+
+/* Style the buttons inside the tab */
+div.tab button {
+    display: block;
+    background-color: inherit;
+    color: black;
+    padding: 22px 16px;
+    width: 100%;
+    border: none;
+    outline: none;
+    text-align: left;
+    cursor: pointer;
+    transition: 0.3s;
+    font-size: 17px;
+}
+
+/* Change background color of buttons on hover */
+div.tab button:hover {
+    background-color: #ddd;
+}
+
+/* Create an active/current "tab button" class */
+div.tab button.active {
+    background-color: #1acefc;
+}
+
+/* Style the tab content */
+.tabcontent {
+    float: left;
+    padding: 0px 12px;
+    border: 1px solid #ccc;
+    width: 80%;
+    min-height: 250px;
+}
+</style>
+</head>
+<body>
+
+<p>Welcome to CRESSdna.org</p>
+
+<div class="tab">
+  <button class="tablinks" onclick="openTab(event, 'Home')" id="defaultOpen">Home</button>
+  <button class="tablinks" onclick="openTab(event, 'Taxonomy')">Taxonomy</button>
+  <button class="tablinks" onclick="openTab(event, 'Contact')">Contact</button>
+  <button class="tablinks" onclick="openTab(event, 'Results')">Results</button>
+ </div>
+
+<div id="Home" class="tabcontent">
+  <h3>Home</h3>
+  <p>Part of the <a href='http://www.nsf.gov/pubs/2010/nsf10513/nsf10513.htm'>National Science Foundation's Assembling the Tree of Life</a>.</p>
+    <img src='nsf1.jpg' alt='Sponsored with a Grant from the National Science Foundation'>
+</div>
+
+<div id="Taxonomy" class="tabcontent">
+  <h3>Taxonomy</h3>
+  <p>Please enter only one word as the name(no space) and only one Rep sequence</p>
+  <form action="./cgi-bin/classifier.py" method="post"><br>
+	<input type="text" name="seqname" value="seqID"><br>
+	<textarea rows="4" cols="50" name="fasta" input type="submit">
+Enter ONE Rep protein sequence here...</textarea>
+			<br>
+		<input type="reset">
+		<input type="submit">
+</form>	
+  		<p>
+  			<ul>
+	<li>This classifier requires Rep protein sequence to be:</li>
+		<ul>
+		<li>Complete</li>
+		<li>Unaligned</li>
+		<li>in FASTA format</li>
+		</ul>
+	<p>And has been trained on the following Genera:</p>
+		<li>Circoviridae</li>	
+			<ul>
+			<li>Circovirus</li>
+			<li>Cyclovirus</li>
+			</ul>
+		<li>Nanoviridae</li>
+			<ul>
+			<li>Babuvirus</li>
+			<li>Nanovirus</li>
+			</ul>
+		<li>Genomoviridae</li>	
+			<ul>
+			<li>Gemycircularvirus</li>
+			<li>Gemygorvirus</li>
+			<li>Gemykibivirus</li>
+			<li>Gemykolovirus</li>
+			<li>Gemykrogvirus</li>
+			<li>Gemyvongvirus</li>
+			</ul>
+		<li>Geminiviridae</li>
+			<ul>
+			<li>Becurtovirus</li>
+			<li>Begomovirus</li>
+			<li>Capulavirus</li>
+			<li>Curtovirus</li>
+			<li>Eragrovirus</li>
+			<li>Grablovirus</li>
+			<li>Mastrevirus</li>
+			<li>Turncurtovirus</li>
+			</ul>
+		<li>Smacovirus</li>
+</ul>  		</p>
+</div>
+
+
+<div id="Contact" class="tabcontent">
+  <h3>Contact</h3>
+  <p>Questions or comments? Send us an email:</p>
+	<p>email At domain Dot something</p>
+</div> 
+
+<div id="Results" class="tabcontent">
+  <h3>Results</h3>
+  <p>Results from Taxonomy prediction</p>
+</div> 
+ 
+<script>
+function openTab(evt, tabTitle) {
+    var i, tabcontent, tablinks;
+    tabcontent = document.getElementsByClassName("tabcontent");
+    for (i = 0; i < tabcontent.length; i++) {
+        tabcontent[i].style.display = "none";
+    }
+    tablinks = document.getElementsByClassName("tablinks");
+    for (i = 0; i < tablinks.length; i++) {
+        tablinks[i].className = tablinks[i].className.replace(" active", "");
+    }
+    document.getElementById(tabTitle).style.display = "block";
+    evt.currentTarget.className += " active";
+}
+
+// Get the element with id="defaultOpen" and click on it
+document.getElementById("defaultOpen").click();
+</script>
+
+</body>
+</html> 
diff --git a/CRESSresults.html b/CRESSresults.html
new file mode 100644
index 0000000..8a78bcd
--- /dev/null
+++ b/CRESSresults.html
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+<!DOCTYPE html>
+
+<html>
+<head>
+
+</head>
+<body>
+
+<h3>Taxonomy Prediction Results</h3>
+	<p>Results as Name, predicted Genus, length of sequence: </p><br>
+	<input type="text" readonly="true" value={prediction} size="40"/><br><br>
+	<p>This classifier will return the best fit of the submitted sequence to the training data.<br>
+Currently included in the training data:<br>
+<li>Circoviridae</li>	
+			<ul>
+			<li>Circovirus</li>
+			<li>Cyclovirus</li>
+			</ul>
+		<li>Nanoviridae</li>
+			<ul>
+			<li>Babuvirus</li>
+			<li>Nanovirus</li>
+			</ul>
+		<li>Genomoviridae</li>	
+			<ul>
+			<li>Gemycircularvirus</li>
+			<li>Gemygorvirus</li>
+			<li>Gemykibivirus</li>
+			<li>Gemykolovirus</li>
+			<li>Gemykrogvirus</li>
+			<li>Gemyvongvirus</li>
+			</ul>
+		<li>Geminiviridae</li>
+			<ul>
+			<li>Becurtovirus</li>
+			<li>Begomovirus</li>
+			<li>Capulavirus</li>
+			<li>Curtovirus</li>
+			<li>Eragrovirus</li>
+			<li>Grablovirus</li>
+			<li>Mastrevirus</li>
+			<li>Turncurtovirus</li>
+			</ul>
+		<li>Smacovirus</li>
+	
+	<a href="./www/html/CRESSdna.html">Return to CRESSdna.org</a>
+</p>	
+
+</body>
+</html> 
+
diff --git a/cgi-bin/SVM_linear_aa_clf.pkl b/cgi-bin/SVM_linear_aa_clf.pkl
new file mode 100644
index 0000000..1afce0a
--- /dev/null
+++ b/cgi-bin/SVM_linear_aa_clf.pkl
diff --git a/cgi-bin/UniqRepsGemys_6089_StSCALER.pkl b/cgi-bin/UniqRepsGemys_6089_StSCALER.pkl
new file mode 100644
index 0000000..3a098bd
--- /dev/null
+++ b/cgi-bin/UniqRepsGemys_6089_StSCALER.pkl
diff --git a/cgi-bin/classifier.py b/cgi-bin/classifier.py
new file mode 100644
index 0000000..ec2b634
--- /dev/null
+++ b/cgi-bin/classifier.py
@@ -0,0 +1,52 @@
+#!/usr/bin/python
+
+#import packages to be used
+from sklearn.svm import SVC
+from sklearn.feature_extraction.text import CountVectorizer
+from sklearn.preprocessing import StandardScaler
+from sklearn.externals import joblib
+import cgi, cgitb
+
+cgitb.enable()
+form=cgi.FieldStorage()
+if form.getvalue('fasta'):
+	alignment = form.getvalue('fasta')
+	alignment=[alignment]
+	name=form.getvalue('seqname')
+	size=len(alignment[0])
+else:
+	alignment = ["MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGHILIECGAPRNQGKRSDLSTAYFDYQQSGPPGMVLLNCCPSCRSSLSEDYYFAILEDCWRTINGGTRRPI"]
+	name='demo'
+	size=len(alignment[0])
+	
+html = open("./www.html/CRESSresults.html")
+page=html.read()
+
+
+AAs=['a','c','d','e','f','g','h','i','k','l','m','n','p','q','r','s','t','v','w','y']
+clf=joblib.load("./cgi-bin/SVM_linear_aa_clf.pkl")
+StSc=joblib.load("./cgi-bin/UniqRepsGemys_6089_StSCALER.pkl")
+cv=CountVectorizer(analyzer='char',ngram_range=(1,1),vocabulary=AAs)
+
+
+#initialize text data vectorizer
+
+dataVect=cv.transform(alignment)
+ 	
+#Scale the data to the training set
+X=StSc.transform(dataVect.astype("float64"))
+
+#make predictions for the original dataset
+results=",".join([name,clf.predict(X)[0]])
+results=",".join([results,str(size)])
+#for i in results:
+	#print(i[0],"\t",i[1])
+
+output = page.format(prediction=results)
+"""f=open('test.html','w')
+f.write(output)
+f.close()"""
+print (output)	
+
+	
+quit()
+\ No newline at end of file