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| author | elavington <elavington@hotmail.com> | 2017-07-27 15:33:17 -0400 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2017-07-27 15:33:17 -0400 |
| commit | 228f8f203eac1b5881d890e266ac10d46bb1b024 (patch) | |
| tree | 6ee415846c8889e94480676c991581b92fa44de6 | |
| parent | 3e5406bbd3e05ac59c1cc954de7bf8187baf9a39 (diff) | |
| download | cressdna-backup.tar.gz cressdna-backup.zip | |
Add files via uploadbackup
| -rw-r--r-- | CRESSdna.html | 156 | ||||
| -rw-r--r-- | CRESSresults.html | 51 | ||||
| -rw-r--r-- | cgi-bin/SVM_linear_aa_clf.pkl | bin | 0 -> 187597 bytes | |||
| -rw-r--r-- | cgi-bin/UniqRepsGemys_6089_StSCALER.pkl | bin | 0 -> 980 bytes | |||
| -rw-r--r-- | cgi-bin/classifier.py | 52 |
5 files changed, 259 insertions, 0 deletions
diff --git a/CRESSdna.html b/CRESSdna.html new file mode 100644 index 0000000..a97d1c1 --- /dev/null +++ b/CRESSdna.html @@ -0,0 +1,156 @@ +<!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 @@ -0,0 +1,51 @@ +<!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 Binary files differnew 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 Binary files differnew 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()
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