diff options
Diffstat (limited to 'bin')
| -rwxr-xr-x | bin/classifier.py | 247 |
1 files changed, 197 insertions, 50 deletions
diff --git a/bin/classifier.py b/bin/classifier.py index ea19333..7cf7912 100755 --- a/bin/classifier.py +++ b/bin/classifier.py @@ -112,60 +112,111 @@ header="""Content-type:text/html <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; +/* Menu Styles */ +.third-level-menu +{ + position: absolute; + top: 0; + right: -150px; + width: 150px; + list-style: none; + padding: 0; + margin: 0; + display: none; } -/* 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; + +.third-level-menu > li +{ + height: 30px; + background: #ddd; } -/* Change background color of buttons on hover */ -div.tab button:hover { - background-color: #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; } -/* Create an active/current "tab button" class */ -div.tab button.active { - background-color: #1acefc; + +.second-level-menu > li +{ + position: relative; + height: 30px; + background: #ddd; } -/* Style the tab content */ -.tabcontent { - float: left; - padding: 0px 12px; - border: 1px solid #ccc; - width: 80%; - min-height: 250px; +.second-level-menu > li:hover { background: #1acefc; } + +.top-level-menu +{ + list-style: none; + padding: 0; + margin: 0; } -table { - border-collapse: collapse; - width: 80%; + +.top-level-menu > li +{ + position: relative; + float: left; + height: 30px; + width: 150px; + background: #ddd; } +.top-level-menu > li:hover { background: #1acefc; } -th, td { - text-align: left; - padding: 8px; +.top-level-menu li:hover > ul +{ + /* On hover, display the next level's menu */ + display: inline; } -tr:nth-child(even){background-color: #f2f2f2} -th { - background-color: #ff0000; +/* 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> @@ -175,12 +226,27 @@ 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> +<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> @@ -188,7 +254,81 @@ body1="""<body> <img src='../nsf1.jpg' alt='Sponsored with a Grant from the National Science Foundation'> </div> -<div id="Taxonomy" class="tabcontent"> +<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="classifier.py" method="post"><br> <textarea rows="4" cols="50" name="fasta" input type="submit"> @@ -248,6 +388,13 @@ MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHI </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> @@ -255,7 +402,7 @@ 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><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> |