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| -rw-r--r-- | classifier2.py | 509 |
1 files changed, 509 insertions, 0 deletions
diff --git a/classifier2.py b/classifier2.py new file mode 100644 index 0000000..3ada9b8 --- /dev/null +++ b/classifier2.py @@ -0,0 +1,509 @@ +#!/home/erik/bin/python3
+
+#%% Load libraries
+import cgi, cgitb
+from sklearn.externals import joblib
+import pandas as pd
+import numpy as np
+from keras.models import Sequential, load_model
+from keras.layers import Embedding, Conv1D, Dense, Flatten
+from keras.initializers import RandomNormal
+from keras.optimizers import RMSprop
+from keras.preprocessing.text import one_hot
+from keras.preprocessing.sequence import pad_sequences
+from sklearn.preprocessing import LabelEncoder
+from sklearn.model_selection import train_test_split
+from keras.utils import to_categorical
+
+#----------------------------------------------\
+# Parse the web-form information to variables \
+# \_______________________________________________________
+# |
+cgitb.enable(display=1, logdir="/var/www/html/bin/")
+form=cgi.FieldStorage()
+alignment = form.getvalue('fasta')
+if alignment.startswith(">"): #naive check for FASTA format
+ list=alignment.split(">")
+ if list[0] == "":
+ list.pop(0)#get rid of the leading empty string
+
+ seqList=[]
+ lenList=[]
+ nameList=[]
+
+ 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=['AAF97593.1']
+ lenList=[str(len(alignment[0]))]
+
+else:
+ seqList = ["MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGHILIECGAPRNQGKRSDLSTAYFDYQQSGPPGMVLLNCCPSCRSSLSEDYYFAILEDCWRTINGGTRRPI"]
+ nameList=['AAF97593.1']
+#%% Constants for the models
+max_len=573
+lenList=[str(len(alignment[0]))]
+
+#%%load the models
+GeneModel=load_model("./GeneModel.model")
+GenusModel=load_model("./Gene_Rep_vs_Other.model")
+le=joblib.load("./LabelEncoder.pkl")
+
+#%%transfrom the input for the models
+X=[" ".join(seq) for seq in seqList]
+X=[one_hot(x,26, lower=False) for x in X]
+X=[one_hot(x,n=26,lower=False) for x in X]
+X=pad_sequences(X,maxlen=max_len,value=0,padding="post")
+
+#%% make predictions
+rep_pred=GeneModel.predict_classes(X)
+genus_prob=[max(x) for x in GenusModel.predict(X)]
+genus_pred=GenusModel.predict_classes(X)
+
+
+#----------------------------------------------\
+# Build HTML table of results \
+# \_______________________________________________________
+#
+#results="<p> Entered Text Content Seq Name is {0} length {1}</p>".format(nameList,predictions)
+resultsTable=""
+resultsTable+="""
+<table>
+<tr>
+<th>Sequence Name</th>
+<th>Length</th>
+<th>Rep?</th>
+<th>Predicted Genus</th>
+<th>Genus Probability</th>
+</tr>
+
+"""
+
+
+for k in range(len(nameList)):
+ resultsTable+="<tr><td>{0}</td><td>{1}</td><td>{2}</td></tr>".format(nameList[k],lenList[k],rep_pred[k],genus_pred[k],genus_prob[k])
+
+resultsTable+="</table>"
+
+
+#----------------------------------------------\
+# Build output page \
+# \_______________________________________________________
+# |
+#build output page parts
+#Header and CSS Style bits
+
+header="""Content-type:text/html
+
+<html>
+<head>
+<meta name="description" content="Home of CRESS virus" />
+<title>CRESS virus home</title>
+<meta name="robots" content="nofollow, nosnippet" />
+<link rel="stylesheet" type="text/css" href="./bin/mystyle.css">
+</head>
+
+"""
+#----------------------------------------------\
+# Build output page \
+# \_______________________________________________________
+# |
+#build output page parts
+#Header and CSS Style bits
+
+header="""Content-type:text/html
+
+<html>
+<head>
+<style>
+*{box-sizing: border-box;}
+body {font-family: "Lato", sans-serif;}
+/* Menu Styles */
+.third-level-menu
+{
+ position: absolute;
+ top: 0;
+ right: -150px;
+ width: 150px;
+ list-style: none;
+ padding: 0;
+ margin: 0;
+ display: none;
+}
+
+.third-level-menu > li
+{
+ height: 30px;
+ background: #ddd;
+}
+.third-level-menu > li:hover { background: #1acefc; }
+
+.second-level-menu
+{
+ position: absolute;
+ top: 30px;
+ left: 0;
+ width: 150px;
+ list-style: none;
+ padding: 0;
+ margin: 0;
+ display: none;
+}
+
+.second-level-menu > li
+{
+ position: relative;
+ height: 30px;
+ background: #ddd;
+}
+.second-level-menu > li:hover { background: #1acefc; }
+
+.top-level-menu
+{
+ list-style: none;
+ padding: 0;
+ margin: 0;
+}
+
+.top-level-menu > li
+{
+ position: relative;
+ float: left;
+ height: 30px;
+ width: 150px;
+ background: #ddd;
+}
+.top-level-menu > li:hover { background: #1acefc; }
+
+.top-level-menu li:hover > ul
+{
+ /* On hover, display the next level's menu */
+ display: inline;
+}
+
+
+/* Menu Link Styles */
+
+.top-level-menu a /* Apply to all links inside the multi-level menu */
+{
+ font: bold 14px Arial, Helvetica, sans-serif;
+ color: black;
+ text-decoration: none;
+ padding: 0 0 0 10px;
+
+ /* Make the link cover the entire list item-container */
+ display: block;
+ line-height: 30px;
+}
+.top-level-menu a:hover { color: black; }
+
+.tabcontent {
+ float: left;
+ padding: 0px 12px;
+ border: 1px solid #ccc;
+ width: 100%;
+ min-height: 250px;
+}
+table {
+ font-family: arial, sans-serif;
+ border-collapse: collapse;
+ width: 50%;
+}
+
+th{
+ background-color: red;
+ color: white;
+}
+td, th {
+ border: 1px solid #dddddd;
+ text-align: left;
+ padding: 8px;
+}
+
+tr:nth-child(even) {
+ background-color: #dddddd;
+}
+</style>
+</head>
+
+"""
+#Page contents, first part
+body1="""<body>
+
+<p>Welcome to CRESSdna.org</p>
+
+<ul class="top-level-menu">
+ <li><a href="#" class="tablinks" onclick="openTab(event, 'Home')" >Home</a></li>
+ <li>
+ <a href="#">Taxonomy</a>
+ <ul class="second-level-menu">
+ <li><a href="#" class="tablinks" onclick="openTab(event, 'Circoviridae')">Circoviridae</a></li>
+ <li><a href="#" class="tablinks" onclick="openTab(event, 'Nanoviridae')">Nanoviridae</a></li>
+ <li><a href="#"><i>more on the way</i></a></li>
+ </ul>
+ </li>
+ <li>
+ <a href="#">Classifier</a>
+ <ul class="second-level-menu">
+ <li><a href="#" class="tablinks" onclick="openTab(event, 'Classifier')">Run the classifier</a></li>
+ <li><a href="#" class="tablinks" onclick="openTab(event, 'Results')" id="defaultOpen">Results</a></li>
+ </ul>
+ </li>
+ <li><a href="#" class="tablinks" onclick="openTab(event, 'Contributers')">Contributers</a></li>
+ <li><a href="#" class="tablinks" onclick="openTab(event, 'Contact')">Contact</a></li>
+
+</ul>
+
+<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="Circoviridae" class="tabcontent">
+ <h3><i>Circoviridae</i></h3>
+<p>
+<br>
+Many animal-infecting CRESS-DNA viruses are classified into the <a href="http://jgv.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.000871"><i>Circoviridae</i> family</a>. There are two genera within the group, the older <i>Circovirus</i> and the more recently codified <i>Cyclovirus</i>, but both are well represented. At least one disease of economic importance is associated with circovirus infections: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652492/">post-weaning maturation wasting syndrome</a> in pigs (caused in part by porcine circovirus 2, which is now largely controlled through <a hfref="https://www.ncbi.nlm.nih.gov/pubmed/27769529">vaccination in commercial hog production</a>). However, several worldwide veterinary diseases are due to circoviruses, including <a href="https://en.wikipedia.org/wiki/Psittacine_beak_and_feather_disease">beak and feather disease</a> and <a href="https://www.ncbi.nlm.nih.gov/pubmed/28242782">fatal acute diarrhea</a> in dogs.
+</p>
+<figure>
+ <img class=scaled src="../DogCV.png", alt='missing' />
+ <figcaption><a href="https://wwwnc.cdc.gov/eid/article/19/4/12-1390-f2">Gastrointestinal system of dogs infected with dog circovirus</a> (DogCV) with hemorrhaging in stomach and intestines. CC-BY Li et al. 2013</figcaption>
+</figure>
+<figure>
+ <img class=scaled src="../PCV2.jpg", alt='missing' />
+ <figcaption><a href="https://virologyj.biomedcentral.com/articles/10.1186/1743-422X-8-291">Immune electron microscopy image of PCV2</a> (porcine circovirus 2) particles. CC-BY Guo et al. 2011</figcaption>
+</figure>
+<p>
+While some of the environmental isolates assigned to <i>Circoviridae</i> have genomes over 3,000 and 4,000 bases, it also contains some of the smallest genomes of CRESS-DNA viruses - some well-studied circoviruses have genomes about 1700nt long, and circularized putative genomes from metagenomics studies can be even smaller. Most analyzed sequences have two ORFs: the replication-associated protein (Rep, also referred to as the replication initiator protein) and capsid protein (Cp or Cap), with some isolates having had a third ORF experimentally verified, and some sequences having many hypothetical ORFs called that have not yet been studied in the lab.
+</p>
+<p>
+Both cycloviruses and circoviruses have non-enveloped, icosahedral virions of 15-25nm encapsidating their circular, ssDNA genomes, but while members of <i>Circovirus</i> are found infecting or associated with mammals, birds and fish, cycloviruses have been found infecting or associated with mammals, birds and insects. Sequences assigned to <i>Circovirus</i> have ambisense genomes, with the Rep gene in sense, sequences in Cyclovirus typically are ambisense in the opposite orientation (Rep gene in anti-sense).
+</p>
+<p>
+A great <a href="http://jgv.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.000871">primer</a> on <i>Circoviridae</i>
+</p>
+<p>
+For more information about <i>Circovirus</i>:
+<br>
+<a href="https://talk.ictvonline.org/ictv-reports/ictv_online_report/ssdna-viruses/w/circoviridae/659/genus-circovirus">ICTV report</a> on circovirus<br>
+<a href="https://viralzone.expasy.org/118">ExPASy ViralZone summary of circovirus</a>
+Type species: <i>Porcine circovirus</i> 1 (<a href="https://www.ncbi.nlm.nih.gov/nuccore/12280941">NC_001792.2</a>)
+</p>
+<p>
+For more information about <i>Cyclovirus</i>:
+<br>
+<a href="https://talk.ictvonline.org/ictv-reports/ictv_online_report/ssdna-viruses/w/circoviridae/660/genus-cyclovirus">ICTV report</a> on cyclovirus<br>
+<a href="https://viralzone.expasy.org/7296">ExPASy ViralZone summary of cyclovirus</a>
+Type species: <i>Human-associated cyclovirus 8</i> (<a href="https://www.ncbi.nlm.nih.gov/nuccore/KF031466">KF031466</a>)
+</p>
+</div>
+
+<div id="Nanoviridae" class="tabcontent">
+<h3><i>Nanoviridae</i></h3>
+<p>
+The plant infecting CRESS-DNA viruses with more than two genomic segments belong in the family <a href="https://talk.ictvonline.org/ictv-reports/ictv_9th_report/ssdna-viruses-2011/w/ssdna_viruses/149/nanoviridae"><i>Nanoviridae</i></a>, which includes the genera <i>Babuvirus</i> and <i>Nanovirus</i>. One of the most economically important species in the family <i>Nanoviridae</i> is Banana bunchy top virus (BBTV), the type species of babuvirus. BBTV causes <a href="http://www.promusa.org/Bunchy+top">banana bunchy top disease</a>, which is common in banana growing areas such as Southeast Asia, the South Pacific, India and Africa. This virus is transmitted by the banana aphid and causes <a href="http://www.musarama.org/en/image/bunchy-top-symptom-81.html">plant crumpling, shrinking and chlorosis</a>, which may develop into necrosis.
+<br>
+<figure>
+ <img class=scaled src="../bbv.jpg", alt='missing', width="512", height="384"/>
+ <figcaption>Banana bunchy top, caused by Banana bunchy top virus (BBTV). CC-BY Scott Nelson 2014.</figcaption>
+</figure>
+
+<p>
+Viruses in the Family Nanoviridae have <a href="https://talk.ictvonline.org/ictv-reports/ictv_9th_report/ssdna-viruses-2011/w/ssdna_viruses/149/nanoviridae">multipartite genomes</a> consisting of 6 to 8 ~1000 nucleotide segments of circular ssDNA. Five of these DNA components are shared between babuviruses and nanoviruses. <a href="https://talk.ictvonline.org/ictv-reports/ictv_9th_report/ssdna-viruses-2011/w/ssdna_viruses/150/nanoviridae-figures">(DNA-R, -N, -S, -C and -M)</a>. Nanoviruses infect <a href="http://theseedsite.co.uk/monocots2.html">dicots</a>, have 8 genomic DNAs and may include three other DNA components with functions that have yet to be determined (DNA-U1, -U2 and U-4). Babuviruses infect <a href="http://theseedsite.co.uk/monocots2.html">monocots</a>, have 6 genomic DNAs and may include another DNA component with an unknown function (DNA-U4). Each of these components encode a single ORF that is transcribed in one direction, thogh a second putative ORF has been identified on one segment of BBTV (DNA-R). The virions are non-enveloped, sized 17-20nm in diameter and have on CP (coat protein). Additional DNA segments (alphasatellites) are also associated with many viruses in the family and can alter disease symptoms.
+</p>
+
+<p>
+For more information about Nanovirus:
+<br>
+<a href="https://talk.ictvonline.org/ictv-reports/ictv_9th_report/ssdna-viruses-2011/w/ssdna_viruses/149/nanoviridae">ICTV report</a> on nanovirus.
+<br>
+<a href="https://viralzone.expasy.org/565?outline=all_by_species">ExPASy ViralZone summary of nanovirus</a>
+<br>
+Type Species: <i>Subterranean clover stunt virus</i> (<a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_003818.1">NC_003818.1</a>)
+</p>
+
+<p>
+For more information about Babuvirus:
+<br>
+<a href="https://talk.ictvonline.org/ictv-reports/ictv_9th_report/ssdna-viruses-2011/w/ssdna_viruses/149/nanoviridae">ICTV report</a> on babuvirus.
+<br>
+<a href="https://viralzone.expasy.org/564?outline=all_by_species">ExPASy ViralZone summary of babuvirus</a>
+<br>
+Type Species: <i>Banana bunchy top virus</i> (<a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_003479.1">NC_003479.1</a>)
+</p>
+</div>
+
+<div id="Classifier" class="tabcontent">
+ <h3>Taxonomy</h3>
+ <form action="classifier2.py" method="post"><br>
+ <textarea rows="4" cols="50" name="fasta" input type="submit">
+>Demo
+MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGHILIECGAPRNQGKRSDLSTAYFDYQQSGPPGMVLLNCCPSCRSSLSEDYYFAILEDCWRTINGGTRRPI</textarea>
+</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><strike>Gemyvongvirus</strike></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>
+ <li>Huchismacovirus</li>
+ <li>Porprismacovirus</li>
+ </ul>
+ <li>Bacilladnaviridae</li>
+ <ul>
+ <li>Protobacilladnavirus</li>
+ </ul>
+</ul> </p>
+</div>
+<div id="Contact" class="tabcontent">
+ <h3>Contact</h3>
+ <p>This site is under construction</p>
+ <p>Please be patient while we tidy up a bit!</p>
+
+</div>
+
+<div id="Contributers" class="tabcontent">
+ <h3>Contributors</h3>
+ <p>This site is under construction</p>
+ <p>Please be patient while we tidy up a bit!</p>
+
+</div>
+
+<div id="Results" class="tabcontent">
+ <h3>Results</h3>
+ <p>Results from Taxonomy prediction</p>
+
+"""
+
+#Page contents, second part (results fit between body1 and body2)
+body2="""<p><br><br>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><strike>Gemyvongvirus</strike></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>
+ <li>Huchismacovirus</li>
+ <li>Porprismacovirus</li>
+ </ul>
+ <li>Bacilladnaviridae</li>
+ <ul>
+ <li>Protobacilladnavirus</li>
+ </ul>
+<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
+
+#build the output page
+page=header+body1+home+aboutus+classifier+circovirus+contact+results1+resultsTable+results2+body2+footer
+
+#send the output as html
+print (page)
+quit()
+
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