diff options
Diffstat (limited to 'bin')
| -rwxr-xr-x | bin/classifier.py | 180 |
1 files changed, 92 insertions, 88 deletions
diff --git a/bin/classifier.py b/bin/classifier.py index e3150ee..2766f08 100755 --- a/bin/classifier.py +++ b/bin/classifier.py @@ -1,47 +1,52 @@ -#!/home/erik/bin/python3.6 +#!/home/erik/bin/python3 #import packages to be used +import cgi, cgitb +import warnings 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 -import warnings - -warnings.simplefilter("ignore", UserWarning) +import re +warnings.simplefilter("ignore", UserWarning)#ignore a joblib version warning #----------------------------------------------\ # Parse the web-form information to variables \ # \_______________________________________________________ # | -cgitb.enable() +cgitb.enable(display=1, logdir="/var/www/html/bin/") form=cgi.FieldStorage() -alignment = str(form.getvalue('fasta')) +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 + if list[0] == "": + list.pop(0)#get rid of the leading empty string + seqList=[] lenList=[] nameList=[] - for i in book: - nameList.append(i) - seqList.append(book[i]) - lenList.append(str(len(book[i]))) - + + for a in list: + tempList=a.split("\r\n") + if tempList[-1]=="": + tempList.pop(-1)#get rid of the trailing empty string + + tempSeq="" + nameList.append(tempList[0]) + for element in tempList[1:]: + tempSeq+=element + + seqList.append(tempSeq) + lenList.append(str(len(tempSeq))) + if len(seqList)==0: #check for empty sequence list seqList = ["MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGHILIECGAPRNQGKRSDLSTAYFDYQQSGPPGMVLLNCCPSCRSSLSEDYYFAILEDCWRTINGGTRRPI"] - nameList=['demo'] + nameList=['Demo'] lenList=[str(len(alignment[0]))] - + else: seqList = ["MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGHILIECGAPRNQGKRSDLSTAYFDYQQSGPPGMVLLNCCPSCRSSLSEDYYFAILEDCWRTINGGTRRPI"] - nameList=['demo'] + nameList=['Demo'] lenList=[str(len(alignment[0]))] #--------------------------------------------------------------------------------------------------------+ @@ -54,41 +59,44 @@ else: 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("SVM_linear_aa_clf.pkl") -StSc=joblib.load("UniqRepsGemys_6089_StSCALER.pkl") +clf=joblib.load("./SVM_linear_aa_clf.pkl") + +StSc=joblib.load("./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="""""" -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.<br>""" -else: - results+=""" - <table> - <tr> - <th>Sequence Name</th> - <th>Length</th> - <th>Prediction</th> - </tr> - """ - for k in len(seqList): - results+="""<tr><td>{0}</td><td>{1}</td><td>{2}</td></tr>""".format(nameList[k],lenList[k],predictions[k]) - results+=""" - </table> - """ +# +#results="<p> Entered Text Content Seq Name is {0} length {1}</p>".format(nameList,predictions) +results="" +results+=""" +<table> +<tr> +<th>Sequence Name</th> +<th>Length</th> +<th>Prediction</th> +</tr> + +""" + + +for k in range(len(nameList)): + results+="<tr><td>{0}</td><td>{1}</td><td>{2}</td></tr>".format(nameList[k],lenList[k],predictions[k]) + +results+="</table>" + #----------------------------------------------\ # Build output page \ @@ -96,7 +104,8 @@ else: # | #build output page parts #Header and CSS Style bits -header="""<!DOCTYPE html> + +header="""Content-type:text/html <html> <head> @@ -105,66 +114,64 @@ header="""<!DOCTYPE html> body {font-family: "Lato", sans-serif;} /* Style the tab */ div.tab { - float: left; - border: 1px solid #ccc; - background-color: #f1f1f1; - width: 20%; - height: 250px; + 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; + 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; + background-color: #ddd; } /* Create an active/current "tab button" class */ div.tab button.active { - background-color: #1acefc; + background-color: #1acefc; } /* Style the tab content */ .tabcontent { - float: left; - padding: 0px 12px; - border: 1px solid #ccc; - width: 80%; - min-height: 250px; + float: left; + padding: 0px 12px; + border: 1px solid #ccc; + width: 80%; + min-height: 250px; } table { - border-collapse: collapse; - width: 80%; + border-collapse: collapse; + width: 80%; } th, td { - text-align: left; - padding: 8px; + text-align: left; + padding: 8px; } tr:nth-child(even){background-color: #f2f2f2} th { - background-color: #ff0000; - color: white; + background-color: #ff0000; + color: white; } - </style> </head> -""" +""" #Page contents, first part -body1=""" -<body> +body1="""<body> <p>Welcome to CRESSdna.org</p> @@ -173,7 +180,7 @@ body1=""" <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')"id="defaultOpen">Results</button> - </div> +</div> <div id="Home" class="tabcontent"> <h3>Home</h3> @@ -236,8 +243,9 @@ MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHI </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> + <p>This site is under construction</p> + <p>Please be patient while we tidy up a bit!</p> + </div> <div id="Results" class="tabcontent"> @@ -247,8 +255,7 @@ MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHI """ #Page contents, second part (results fit between body1 and body2) -body2=""" - <p>This classifier will return the best fit of the submitted sequence to the training data.<br> +body2="""<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> @@ -307,14 +314,11 @@ document.getElementById("defaultOpen").click(); #close the Page footer=""" -</html> -""" +</html>""" #build the output page page=header+body1+results+body2+footer - + #send the output as html -#output = page.format() print (page) - quit() |