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| author | elavington <elavington@hotmail.com> | 2017-09-25 12:50:03 -0400 |
|---|---|---|
| committer | elavington <elavington@hotmail.com> | 2017-09-25 12:50:03 -0400 |
| commit | 1475085bf6cc046260e570cd53cc590201f66b40 (patch) | |
| tree | 92f397ddb916f0ae1a893d7195159f1710b43ff6 /classifier.py | |
| parent | 0a13a6387b7a9f70ae58fdcd7196b7c480be40bd (diff) | |
| download | cressdna-1475085bf6cc046260e570cd53cc590201f66b40.tar.gz cressdna-1475085bf6cc046260e570cd53cc590201f66b40.zip | |
Remove unwanted files
Diffstat (limited to 'classifier.py')
| -rw-r--r-- | classifier.py | 313 |
1 files changed, 0 insertions, 313 deletions
diff --git a/classifier.py b/classifier.py deleted file mode 100644 index ecf7c15..0000000 --- a/classifier.py +++ /dev/null @@ -1,313 +0,0 @@ -#!/home/erik/bin/python3.6
-
-#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
-
-#----------------------------------------------\
-# Parse the web-form information to variables \
-# \_______________________________________________________
-# |
-cgitb.enable()
-form=cgi.FieldStorage()
-alignment = form.getvalue('fasta')
-if alignment.startswith(">"): #naive check for FASTA format
- list=alignment.split(">")
- book={}
- for a in list:
- tempList=a.splitlines()
- nameLine=tempList.pop(0)
- name=nameLine.split(" ")[0]
- seq="".join(tempList)
- book[name]=seq
- seqList=[]
- lenList=[]
- nameList=[]
- for i in book:
- nameList.append(i)
- seqList.append(book[i])
- lenList.append(str(len(book[i])))
-
- if len(seqList)=0: #check for empty sequence list
- seqList = ["MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGHILIECGAPRNQGKRSDLSTAYFDYQQSGPPGMVLLNCCPSCRSSLSEDYYFAILEDCWRTINGGTRRPI"]
- nameList=['demo']
- lenList=[str(len(alignment[0]))]
-
-else:
- seqList = ["MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGHILIECGAPRNQGKRSDLSTAYFDYQQSGPPGMVLLNCCPSCRSSLSEDYYFAILEDCWRTINGGTRRPI"]
- nameList=['demo']
- lenList=[str(len(alignment[0]))]
-
-#--------------------------------------------------------------------------------------------------------+
-
-#----------------------------------------------\
-# predict genus of input sequences \
-# \_______________________________________________________
-# |
-#list of amino acids as vocabulary for the CountVectorizer
-AAs=['a','c','d','e','f','g','h','i','k','l','m','n','p','q','r','s','t','v','w','y']
-
-#load the classifier and scaler
-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(seqList)
-
-#Scale the data to the training set
-X=StSc.transform(dataVect.astype("float64"))
-
-#make predictions for the original dataset
-predictions=clf.predict(X)
-
-
-#----------------------------------------------\
-# Build HTML table of results \
-# \_______________________________________________________
-# |
-results=""""""
-for k in len(seqList):
- results+="""<tr><td>{0}</td><td>{1}</td><td>{2}</td></tr>""".format(nameList[k],lenList[k],predictions[k])
-if "demo" in nameList:
- results+="""<p>There seems to have been an error.<br>If you are expecting more than one prediction or
- do not see the name you entered please try the submission form again, making sure that the input is in FASTA format."""
-
-#----------------------------------------------\
-# Build output page \
-# \_______________________________________________________
-# |
-#build output page parts
-#Header and CSS Style bits
-header="""
-<!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;
-}
-table {
- border-collapse: collapse;
- width: 80%;
-}
-
-th, td {
- text-align: left;
- padding: 8px;
-}
-
-tr:nth-child(even){background-color: #f2f2f2}
-
-th {
- background-color: #ff0000;
- color: white;
-}
-
-</style>
-</head>
-"""
-
-#Page contents, first part
-body1="""
-<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>
- <table>
- <tr>
- <th>Sequence Name</th>
- <th>Length</th>
- <th>Prediction</th>
- </tr>
-"""
-
-#Page contents, second part (results fit between body1 and body2)
-body2="""
-</table>
- <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>
-<br><br>
-</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>
-"""
-
-#close the Page
-footer="""
-</html>
-"""
-
-#build the output page
-page=header+body1+results+body2+footer
-
-#send the output as html
-output = page.format()
-print (output)
-
-quit()
\ No newline at end of file |