diff options
| -rw-r--r-- | bin/.htaccess | 2 | ||||
| -rw-r--r-- | bin/SVM_linear_aa_clf.pkl (renamed from SVM_linear_aa_clf.pkl) | bin | 187597 -> 187597 bytes | |||
| -rw-r--r-- | bin/UniqRepsGemys_6089_StSCALER.pkl (renamed from UniqRepsGemys_6089_StSCALER.pkl) | bin | 980 -> 980 bytes | |||
| -rwxr-xr-x | bin/classifier.py (renamed from cgi-bin/classifier.py) | 626 | ||||
| -rw-r--r-- | cgi-bin/SVM_linear_aa_clf.pkl | bin | 187597 -> 0 bytes | |||
| -rw-r--r-- | cgi-bin/UniqRepsGemys_6089_StSCALER.pkl | bin | 980 -> 0 bytes | |||
| -rw-r--r-- | index.html | 2 |
7 files changed, 316 insertions, 314 deletions
diff --git a/bin/.htaccess b/bin/.htaccess new file mode 100644 index 0000000..698afb4 --- /dev/null +++ b/bin/.htaccess @@ -0,0 +1,2 @@ +Options +ExecCGI +SetHandler cgi-script diff --git a/SVM_linear_aa_clf.pkl b/bin/SVM_linear_aa_clf.pkl Binary files differindex 1afce0a..1afce0a 100644 --- a/SVM_linear_aa_clf.pkl +++ b/bin/SVM_linear_aa_clf.pkl diff --git a/UniqRepsGemys_6089_StSCALER.pkl b/bin/UniqRepsGemys_6089_StSCALER.pkl Binary files differindex 3a098bd..3a098bd 100644 --- a/UniqRepsGemys_6089_StSCALER.pkl +++ b/bin/UniqRepsGemys_6089_StSCALER.pkl diff --git a/cgi-bin/classifier.py b/bin/classifier.py index ecf7c15..0ae13b5 100755 --- a/cgi-bin/classifier.py +++ b/bin/classifier.py @@ -1,313 +1,313 @@ -#!/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 +#!/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')" >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')"id="defaultOpen">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() diff --git a/cgi-bin/SVM_linear_aa_clf.pkl b/cgi-bin/SVM_linear_aa_clf.pkl Binary files differdeleted file mode 100644 index 1afce0a..0000000 --- a/cgi-bin/SVM_linear_aa_clf.pkl +++ /dev/null diff --git a/cgi-bin/UniqRepsGemys_6089_StSCALER.pkl b/cgi-bin/UniqRepsGemys_6089_StSCALER.pkl Binary files differdeleted file mode 100644 index 3a098bd..0000000 --- a/cgi-bin/UniqRepsGemys_6089_StSCALER.pkl +++ /dev/null @@ -64,7 +64,7 @@ div.tab button.active { <div id="Taxonomy" class="tabcontent"> <h3>Taxonomy</h3> - <form action="./cgi-bin/classifier.py" method="post"><br> + <form action="bin/classifier.py" method="post"><br> <textarea rows="4" cols="50" name="fasta" input type="submit"> >Demo MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGHILIECGAPRNQGKRSDLSTAYFDYQQSGPPGMVLLNCCPSCRSSLSEDYYFAILEDCWRTINGGTRRPI</textarea> |