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| author | elavington <elavington@hotmail.com> | 2017-09-25 11:43:53 -0400 |
|---|---|---|
| committer | elavington <elavington@hotmail.com> | 2017-09-25 11:43:53 -0400 |
| commit | 0a13a6387b7a9f70ae58fdcd7196b7c480be40bd (patch) | |
| tree | 99de444657a9712cf58bcecb93799a46ab3d1b16 | |
| parent | 47b146536121acc6ac8e3d847be2152500fe3167 (diff) | |
| download | cressdna-0a13a6387b7a9f70ae58fdcd7196b7c480be40bd.tar.gz cressdna-0a13a6387b7a9f70ae58fdcd7196b7c480be40bd.zip | |
Revised Folder contents and classifier code
| -rwxr-xr-x | bin/classifier.py | 25 | ||||
| -rw-r--r-- | index.html | 4 |
2 files changed, 15 insertions, 14 deletions
diff --git a/bin/classifier.py b/bin/classifier.py index 0ae13b5..044c6ca 100755 --- a/bin/classifier.py +++ b/bin/classifier.py @@ -13,7 +13,7 @@ import cgi, cgitb # | cgitb.enable() form=cgi.FieldStorage() -alignment = form.getvalue('fasta') +alignment = str(form.getvalue('fasta')) if alignment.startswith(">"): #naive check for FASTA format list=alignment.split(">") book={} @@ -51,8 +51,8 @@ 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("./cgi-bin/SVM_linear_aa_clf.pkl") -StSc=joblib.load("./cgi-bin/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 @@ -69,12 +69,14 @@ 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]) +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.""" + do not see the name you entered please try the submission form again, making sure that the input is in FASTA format.""" +else: + for k in len(seqList): + results+="""<tr><td>{0}</td><td>{1}</td><td>{2}</td></tr>""".format(nameList[k],lenList[k],predictions[k]) + #----------------------------------------------\ # Build output page \ @@ -82,13 +84,12 @@ if "demo" in nameList: # | #build output page parts #Header and CSS Style bits -header=""" -<!DOCTYPE html> +header="""<!DOCTYPE html> <html> <head> <style> -* {box-sizing: border-box} +*{box-sizing: border-box;} body {font-family: "Lato", sans-serif;} /* Style the tab */ div.tab { @@ -307,7 +308,7 @@ footer=""" page=header+body1+results+body2+footer #send the output as html -output = page.format() -print (output) +#output = page.format() +print (page) quit() @@ -3,7 +3,7 @@ <html> <head> <style> -* {box-sizing: border-box} +*{box-sizing: border-box;} body {font-family: "Lato", sans-serif;} /* Style the tab */ div.tab { @@ -64,7 +64,7 @@ div.tab button.active { <div id="Taxonomy" class="tabcontent"> <h3>Taxonomy</h3> - <form action="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> |