tools

chart/tools.py

@@ -3,6 +3,8 @@ import random
 import time
 
 import pandas as pd
+from Bio import SeqIO
+from Bio.SeqUtils import GC
 
 from Simple_Drawing.settings import BASE_DIR
 
@@ -338,7 +340,7 @@ class="layui-input" style="height: 25px; width:80px;margin-top: 6px">
             for d in self.Basics[title]:
                 parameter = ChartParameter(d)
 
-                if parameter.input_type in ["rgb","hex",'color_name']:
+                if parameter.input_type in ["rgb", "hex", 'color_name']:
                     code += f"""{parameter.name}:{parameter.name},
 """
                 else:
@@ -349,7 +351,7 @@ class="layui-input" style="height: 25px; width:80px;margin-top: 6px">
             for d in self.Senior[title]:
                 parameter = ChartParameter(d)
                 print(parameter.input_type)
-                if parameter.input_type in ["rgb", "hex",'color_name']:
+                if parameter.input_type in ["rgb", "hex", 'color_name']:
                     code += f"""{parameter.name}:{parameter.name},
                 """
                 else:
@@ -381,7 +383,7 @@ class="layui-input" style="height: 25px; width:80px;margin-top: 6px">
             }
         });
         })
-            """ % (i, random_color(), fl,i)
+            """ % (i, random_color(), fl, i)
 
         return code
 
@@ -404,4 +406,68 @@ Treemap = {
 }
 
 
+class Basics(object):
+    def __init__(self, file_path, args):
+        self.args = args
+        self.file_path = file_path
+        self.out_file = []
+        self.f = SeqIO.parse(file_path, "fasta")  # 读取多条序列
 
+    def Sequence_cleaning(self):
+        f = self.f
+        temp = []
+        for i in f:
+            temp.append(f">{i.id}\n{str(i.seq)}")
+        self.out_file.append(["Sequence_cleaning", temp])
+
+    def Sequence_length(self):
+        f = self.f
+        temp = []
+        for i in f:
+            temp.append(f"{i.id}\t{len(i)}")
+        self.out_file.append(["Sequence_length", temp])
+
+    def GC_content(self):
+        f = self.f
+        temp = []
+        for i in f:
+            CONTENT = GC(str(i.seq))
+            temp.append(f"{i.id}\t{CONTENT}")
+        self.out_file.append(["GC_content", temp])
+
+    def Sequence_flip(self):
+        f = self.f
+        temp = []
+        for i in f:
+            temp.append(f">{i.id}\n{str(i.reverse_complement().seq)}")
+        self.out_file.append(["Sequence_flip", temp])
+
+    def Reverse_complementarity(self):
+        f = self.f
+        temp = []
+        for i in f:
+            temp.append(f">{i.id}\n{str(i.complement().seq)}")
+        self.out_file.append(["Reverse_complementarity", temp])
+
+    # def Codon_preference(self):
+    #     f = self.f
+    #     temp = []
+    #     for i in f:
+    #         temp.append(f">{i.id}\n{str(i.complement().seq)}")
+    #     self.out_file.append({"Reverse_complementarity": temp})
+
+    def run(self):
+        for i in self.args.keys():
+            if self.args[i] == "YES":
+                eval(f"self.{self.args[i]}")()
+
+        data = ""
+        for i in self.out_file:
+            for j in i:
+                data += f"\n{'-' * 15}\n{j[0]}\n"
+                data += "\n".join(i[1])
+
+        with open(self.file_path, "w") as f:
+            f.write(data)
+
+        return data

chart/urls.py

@@ -7,7 +7,5 @@ urlpatterns = [
     path('down', views.download),
     url("(.*\.html$)", views.out_page),
     url('up_file', views.up_file),
-    url('tools$', views.tools),
-    url('tools$', views.tools),
     url('(.*)_run', views.chart_run),
 ]

chart/views.py

@@ -122,19 +122,3 @@ def chart_run(request, get_chart_sort):
     return JsonResponse({"img": f"/static/img_eg/show_chart/{file_id}_{k}.png"})
 
 
-def tools(request):
-    file = request.FILES.get("file", None)  # 标题
-    mg = request.POST.get('mg', None)
-    data = ""
-    if file is None and mg is None:
-        return JsonResponse({"http": "内容为空"})
-    if file is None:
-        data = 反向互补序列(mg)
-    else:
-        p = file.read()
-        p.decode(encoding='utf-8')
-        data = 反向互补序列(p.decode(encoding='utf-8'))
-
-        file_path, file_id = path_out("tools")
-        keep_file(data, file_path, ui=1)
-    return JsonResponse({"work_id": file_id})

templates/page/tools.html

@@ -123,6 +123,7 @@
     var form = layui.form;
     var url_up = "{{ url }}"
     var upload = layui.upload
+    var element = layui.element
 
 
     // 页面跳转加载函数
@@ -164,6 +165,7 @@
         temp = $('#main_show')
         temp.empty()
         temp.append(String.raw`{% include 'tools/Basics.html' %}`)
+        basics_run()
         form.render();
     }
 
@@ -172,6 +174,7 @@
         temp = $('#main_show')
         temp.empty()
         temp.append(String.raw`{% include 'tools/pfam.html' %}`)
+        pfam_run()
         form.render();
 
 
@@ -183,6 +186,7 @@
         temp = $('#main_show')
         temp.empty()
         temp.append(String.raw`{% include 'tools/Differential_expression_analysis.html' %}`)
+        Differential_expression_analysis_run()
         form.render();
     }
 
@@ -338,6 +342,124 @@
             ;
         })
     }
+
+
+    function pfam_run() {
+        layui.use(['upload'], function () {
+            var $ = layui.jquery
+                , layer = layui.layer;
+            upload.render({
+                elem: '#select_pfam'
+                , url: url_up + '/tools/' + "pfam"
+                , auto: false
+                , accept: 'file'
+                , data: {
+                    csrfmiddlewaretoken: '{{ csrf_token }}',
+                    b_dom: document.getElementById("b_dom").value,
+                    b_seq: document.getElementById("b_seq").value,
+                    e_dom: document.getElementById("e_dom").value,
+                    e_seq: document.getElementById("e_seq").value,
+                    align: document.getElementById("align").value,
+                    clan_overlap: document.getElementById("clan_overlap").value,
+                }
+                , before: function (obj) { //obj参数包含的信息，跟 choose回调完全一致，可参见上文。
+                    layer.load(1); //上传loading
+                }
+                , bindAction: '#pfam_run'
+                , done: function (res, index) {
+                    layer.closeAll('loading'); //关闭loading
+                    ab = '<a href= "' + url_up + '/chart/down?file_id=' + res.id + "&file_downlode_type=txt&ee=1" + '">' + ' <button type="button" class="layui-btn">downlode</button></a>'
+                    $("#down").append(ab)
+                }
+                , error: function (index, upload) {
+                    layer.closeAll('loading'); //关闭loading
+                }
+            })
+            ;
+        })
+    }
+
+
+    function Differential_expression_analysis_run() {
+
+        var uploadListIns = upload.render({
+            elem: '#testList'
+            , elemList: $('#demoList') //列表元素对象
+            , url: url_up + '/tools/' + "Differential_expression_analysis" //此处用的是第三方的 http 请求演示，实际使用时改成您自己的上传接口即可。
+            , accept: 'file'
+            , multiple: true
+            , number: 10
+            , auto: false
+            , bindAction: '#testListAction'
+            , choose: function (obj) {
+                var that = this;
+                var files = this.files = obj.pushFile(); //将每次选择的文件追加到文件队列
+                //读取本地文件
+                obj.preview(function (index, file, result) {
+                    var tr = $(['<tr id="upload-' + index + '">'
+                        , '<td>' + file.name + '</td>'
+                        , '<td>' + (file.size / 1014).toFixed(1) + 'kb</td>'
+                        , '<td><div class="layui-progress" lay-filter="progress-demo-' + index + '"><div class="layui-progress-bar" lay-percent=""></div></div></td>'
+                        , '<td>'
+                        , '<button class="layui-btn layui-btn-xs demo-reload layui-hide">Re</button>'
+                        , '<button class="layui-btn layui-btn-xs layui-btn-danger demo-delete">del</button>'
+                        , '</td>'
+                        , '</tr>'].join(''));
+
+                    //单个重传
+                    tr.find('.demo-reload').on('click', function () {
+                        obj.upload(index, file);
+                    });
+
+                    //删除
+                    tr.find('.demo-delete').on('click', function () {
+                        delete files[index]; //删除对应的文件
+                        tr.remove();
+                        uploadListIns.config.elem.next()[0].value = ''; //清空 input file 值，以免删除后出现同名文件不可选
+                    });
+
+                    that.elemList.append(tr);
+                    element.render('progress'); //渲染新加的进度条组件
+                });
+            }
+            , data: {
+                csrfmiddlewaretoken: '{{ csrf_token }}',
+                {#b_dom: document.getElementById("b_dom").value,#}
+                {#b_seq: document.getElementById("b_seq").value,#}
+                {#e_dom: document.getElementById("e_dom").value,#}
+                {#e_seq: document.getElementById("e_seq").value,#}
+                {#align: document.getElementById("align").value,#}
+                {#clan_overlap: document.getElementById("clan_overlap").value,#}
+            }
+
+            , done: function (res, index, upload) { //成功的回调
+                var that = this;
+                //if(res.code == 0){ //上传成功
+                var tr = that.elemList.find('tr#upload-' + index)
+                    , tds = tr.children();
+                tds.eq(3).html(''); //清空操作
+                delete this.files[index]; //删除文件队列已经上传成功的文件
+                return;
+                //}
+                this.error(index, upload);
+            }
+            , allDone: function (obj) { //多文件上传完毕后的状态回调
+                console.log(obj)
+            }
+            , error: function (index, upload) { //错误回调
+                var that = this;
+                var tr = that.elemList.find('tr#upload-' + index)
+                    , tds = tr.children();
+                tds.eq(3).find('.demo-reload').removeClass('layui-hide'); //显示重传
+            }
+            , progress: function (n, elem, e, index) {
+                element.progress('progress-demo-' + index, n + '%');
+            }
+        });
+
+
+    }
+
 </script>
 
 

templates/tools/Basics.html

@@ -9,7 +9,7 @@
                 <ul class="layui-tab-title">
 
                     {#                    选项卡#}
-                    <li>orf</li>
+                    <li>Basics</li>
                 </ul>
                 <div class="layui-tab-content" style="height: 100px;">
                     <form class="layui-form" action="">
@@ -69,22 +69,22 @@
                         </div>  <!-- 开关-默认关 -->
 
 
-                        <div class="layui-form-item">
+                        {#                        <div class="layui-form-item">#}
-                            <label class="layui-form-label">Codon preference</label>
+                        {#                            <label class="layui-form-label">Codon preference</label>#}
-                            <div class="layui-input-block">
+                        {#                            <div class="layui-input-block">#}
-                                <input type="checkbox" id="Codon_preference" name="close" lay-skin="switch"
+                        {#                                <input type="checkbox" id="Codon_preference" name="close" lay-skin="switch"#}
-                                       lay-text="ON|OFF">
+                        {#                                       lay-text="ON|OFF">#}
-                            </div>
+                        {#                            </div>#}
-                        </div>  <!-- 开关-默认关 -->
+                        {#                        </div>  <!-- 开关-默认关 -->#}
-
+                        {##}
-
+                        {##}
-                        <div class="layui-form-item">
+                        {#                        <div class="layui-form-item">#}
-                            <label class="layui-form-label">Codon frequency</label>
+                        {#                            <label class="layui-form-label">Codon frequency</label>#}
-                            <div class="layui-input-block">
+                        {#                            <div class="layui-input-block">#}
-                                <input type="checkbox" id="Codon_frequency" name="close" lay-skin="switch"
+                        {#                                <input type="checkbox" id="Codon_frequency" name="close" lay-skin="switch"#}
-                                       lay-text="ON|OFF">
+                        {#                                       lay-text="ON|OFF">#}
-                            </div>
+                        {#                            </div>#}
-                        </div>  <!-- 开关-默认关 -->
+                        {#                        </div>  <!-- 开关-默认关 -->#}
 
                         <div class="layui-form-item">
 

templates/tools/Differential_expression_analysis.html

@@ -1,52 +1,84 @@
-<div class='layui-row' style="margin: 50px">
+<div class="layui-bg-gray" style="float: left; padding: 30px; width:45%">
-    <div class='layui-col-md9'>
-        <h1 style="font-size: 50px">Differential expression analysis</h1>
-    </div>
 
-</div>
+    <div class="layui-panel">
+        <div style="padding: 20px 30px;">
 
 
-<div class='layui-row' style="margin-top: 80px; margin-left: 80px">
+            {#            选项#}
+            <div class="layui-tab layui-tab-brief " lay-filter="docDemoTabBrief" style="width: 100%; height: 1000px">
+                <ul class="layui-tab-title">
 
-    <div class='layui-col-md9 layui-form-pane'>
+                    {#                    选项卡#}
-        <fieldset class="layui-elem-field layui-field-title" style="margin-top: 30px;">
+                    <li>Differential expression analysis</li>
-            <legend>counts文件</legend>
+                </ul>
-        </fieldset>
+                <div class="layui-tab-content" style="height: 100px;">
-        <div class="layui-btn-container" style="display: inline-block">
+                    <form class="layui-form" action="">
-            <button type="button" class="layui-btn layui-btn-normal" id="select_file">选择文件</button>
+
+                        <div class="layui-upload">
+                            <button type="button" class="layui-btn layui-btn-normal" id="testList">选择多文件</button>
+                            <div class="layui-upload-list" style="max-width: 1000px;">
+                                <table class="layui-table">
+                                    <colgroup>
+                                        <col>
+                                        <col width="150">
+                                        <col width="260">
+                                        <col width="150">
+                                    </colgroup>
+                                    <thead>
+                                    <tr>
+                                        <th>name</th>
+                                        <th>size</th>
+                                        <th>Upload progress</th>
+                                        <th>operation</th>
+                                    </tr>
+                                    </thead>
+                                    <tbody id="demoList"></tbody>
+                                </table>
+                            </div>
+
+                            <div id="down">
+                                <button type="button" class="layui-btn" id="testListAction">run</button>
+                            </div>
+
+
+                        </div>
+                    </form>
+
+                </div>
+            </div>
         </div>
 
-    </div>
-</div>
-
-<div class='layui-row' style="margin-left: 80px">
-    <div class='layui-col-md9'>
-        <fieldset class="layui-elem-field layui-field-title" style="margin-top: 30px;">
-            <legend>分组文件</legend>
-        </fieldset>
-        <div class="layui-btn-container">
-            <button type="button" class="layui-btn layui-btn-normal" id="select_file">选择文件</button>
-        </div>
 
     </div>
 </div>
-
-<div class='layui-row' style="margin-left: 80px">
-    <div class='layui-col-md9'>
-        <fieldset class="layui-elem-field layui-field-title" style="margin-top: 30px;">
-            <legend>对比文件</legend>
-        </fieldset>
-        <div class="layui-btn-container">
-            <button type="button" class="layui-btn layui-btn-normal" id="select_file">选择文件</button>
-        </div>
-
-    </div>
 </div>
 
-<div class='layui-row' style="margin-left:80px; margin-top: 20px">
+
-    <div class='layui-col-md9'>
+<div class="layui-bg-gray" style="float: left; padding: 30px; width:45%">
-        <div class="layui-btn-container">
+    <div class="layui-panel">
-            <button type="button" class="layui-btn" id="run">RUN</button>
+        <div style="padding: 20px 30px;">
+            <div class="layui-tab layui-tab-brief " lay-filter="docDemoTabBrief" style="width: 100%; height: 1000px">
+                <ul class="layui-tab-title">
+                    <li class="layui-this">function</li>
+                </ul>
+
+                <div class="layui-tab-content">
+                    <div class="layui-tab-item layui-show">
+                        <div style="margin-left: 30px;">
+                            <p style="font-size: 20px">
+
+                                Group file suffix is group<br>
+                                The suffix of the statistics file is con<br>
+                                The suffix of the comparison file is TXT<br>
+
+
+                            </p>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
         </div>
     </div>
 </div>
+

templates/tools/GO.html

@@ -1,67 +1,144 @@
-<div class='layui-row' style="margin: 50px">
+<div class="layui-bg-gray" style="float: left; padding: 30px; width:45%">
-    <div class='layui-col-md9'>
-        <h1 style="font-size: 50px">GO 富集</h1>
-    </div>
 
-</div>
+    <div class="layui-panel">
+        <div style="padding: 20px 30px;">
 
 
-<div class='layui-row' style="margin-top: 80px; margin-left: 80px">
+            {#            选项#}
+            <div class="layui-tab layui-tab-brief " lay-filter="docDemoTabBrief" style="width: 100%; height: 1000px">
+                <ul class="layui-tab-title">
 
-    <div class='layui-col-md9 layui-form-pane'>
+                    {#                    选项卡#}
-        <fieldset class="layui-elem-field layui-field-title" style="margin-top: 30px;">
+                    <li>GO</li>
-            <legend>数据库文件</legend>
+                </ul>
-        </fieldset>
+                <div class="layui-tab-content" style="height: 100px;">
-        <div class="layui-btn-container" style="display: inline-block">
+                    <form class="layui-form" action="">
-            <button type="button" class="layui-btn layui-btn-normal" id="select_file">选择文件</button>
-        </div>
 
-    </div>
+                        <div class="layui-form-item">
-</div>
 
-<div class='layui-row' style="margin-left: 80px">
+                            <div class="layui-btn-container">
-    <div class='layui-col-md9'>
-        <fieldset class="layui-elem-field layui-field-title" style="margin-top: 30px;">
-            <legend>差异表达文件</legend>
-        </fieldset>
-        <div class="layui-btn-container">
-            <button type="button" class="layui-btn layui-btn-normal" id="select_file">选择文件</button>
-        </div>
 
-    </div>
+                                <button type="button" class="layui-btn layui-btn-normal" id="select_orf">select file
-</div>
+                                </button>
-<div class='layui-row' style="margin-left:80px; margin-top: 20px">
+
-    <div class='layui-col-md9'>
+                            </div>
-        <fieldset class="layui-elem-field layui-field-title" style="margin-top: 30px;">
+                        </div>
-            <legend>参数</legend>
+
-        </fieldset>
+                        <div class="layui-form-item">
-        <div class="layui-form-item layui-form layui-form-pane" pane>
+                            <label class="layui-form-label">begin</label>
-            <label class="layui-form-label">logFC阈值</label>
+                            <div class="layui-input-inline">
-            <div class="layui-input-inline">
+                                <input type="text" name="username" id="begin" lay-verify="number" placeholder="请输入"
-                <input type="text" name="logFC" id="logFC" lay-verify="required" placeholder="请输入" autocomplete="off"
+                                       autocomplete="off" class="layui-input">
-                       class="layui-input">
+                            </div>
-            </div>
+                        </div>
-            <label class="layui-form-label">FDR阈值</label>
+
-            <div class="layui-input-inline">
+                        <div class="layui-form-item">
-                <input type="text" name="FDR" id="FDR" lay-verify="required" placeholder="请输入" autocomplete="off"
+                            <label class="layui-form-label">end</label>
-                       class="layui-input">
+                            <div class="layui-input-inline">
-            </div>
+                                <input type="text" name="username" id="end" lay-verify="number" placeholder="请输入"
-            <label class="layui-form-label">GO分类</label>
+                                       autocomplete="off" class="layui-input">
-            <div class="layui-input-inline">
+                            </div>
-                <select name="GO_s">
+                        </div>
-                    <option value="BP" selected>BP</option>
+
-                    <option value="CC">CC</option>
+                        <div class="layui-form-item">
-                    <option value="MF" selected>MF</option>
+                            <label class="layui-form-label">Cyclotype</label>
-                    <option value="ALL">ALL</option>
+                            <div class="layui-input-block">
-                </select>
+                                <input type="checkbox" id="Cyclotype" name="close" lay-skin="switch" lay-text="ON|OFF">
+                            </div>
+                        </div>  <!-- 开关-默认关 -->
+
+
+                        <div class="layui-form-item">
+                            <label class="layui-form-label">Codons</label>
+                            <div class="layui-input-block">
+                                <select name="interest" id="Codons" lay-filter="aihao">
+                                    <option value="0" selected="">0</option>
+                                    <option value="1">1</option>
+                                    <option value="2">2</option>
+                                    <option value="3">3</option>
+                                    <option value="4">4</option>
+                                    <option value="5">5</option>
+                                    <option value="6">6</option>
+                                    <option value="7">7</option>
+                                    <option value="8">8</option>
+                                    <option value="9">9</option>
+                                    <option value="10">10</option>
+                                    <option value="11">11</option>
+                                    <option value="12">12</option>
+                                    <option value="13">13</option>
+                                    <option value="14">14</option>
+                                    <option value="15">15</option>
+                                    <option value="16">16</option>
+                                    <option value="17">17</option>
+                                    <option value="18">18</option>
+                                    <option value="19">19</option>
+                                    <option value="20">20</option>
+                                    <option value="21">21</option>
+                                    <option value="22">22</option>
+                                    <option value="23">23</option>
+                                    <option value="24">24</option>
+                                    <option value="25">25</option>
+                                </select>
+                            </div>
+                        </div>  <!-- 单行选择框 -->
+
+                        <div class="layui-form-item">
+                            <label class="layui-form-label">outfmt</label>
+                            <div class="layui-input-block">
+                                <select name="interest" id="outfmt" lay-filter="aihao">
+                                    <option value="0" selected="">0</option>
+                                    <option value="1">1</option>
+                                    <option value="2">2</option>
+                                    <option value="3">3</option>
+                                </select>
+                            </div>
+                        </div>  <!-- 单行选择框 -->
+
+                        <div class="layui-form-item">
+
+                            <div class="layui-btn-container">
+
+                                <div id="down">
+
+                                    <button type="button" class="layui-btn" id="orf_run">run</button>
+                                    {#                                    <button type="button" class="layui-btn" id="gen_to_fa_down">downlode</button>#}
+                                </div>
+
+                            </div>
+                        </div>
+
+
+                    </form>
+
+                </div>
             </div>
         </div>
+
+
     </div>
 </div>
-<div class='layui-row' style="margin-left:80px; margin-top: 20px">
+</div>
-    <div class='layui-col-md9'>
+
-        <div class="layui-btn-container">
+
-            <button type="button" class="layui-btn" id="run">RUN</button>
+<div class="layui-bg-gray" style="float: left; padding: 30px; width:45%">
+    <div class="layui-panel">
+        <div style="padding: 20px 30px;">
+            <div class="layui-tab layui-tab-brief " lay-filter="docDemoTabBrief" style="width: 100%; height: 1000px">
+                <ul class="layui-tab-title">
+                    <li class="layui-this">function</li>
+                </ul>
+
+                <div class="layui-tab-content">
+                    <div class="layui-tab-item layui-show">
+                        <div style="margin-left: 30px;">
+                            <p style="font-size: 20px">Convert standard gff format files to standard gtf
+                                format</p>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
         </div>
     </div>
 </div>
+

templates/tools/pfam.html

@@ -1,34 +1,128 @@
-<div class='layui-row' style="margin: 50px">
+<div class="layui-bg-gray" style="float: left; padding: 30px; width:45%">
-    <div class='layui-col-md3'>
-        <h1 style="font-size: 50px">Pfam</h1>
-    </div>
-    <div class='layui-col-md9'>
 
-    </div>
+    <div class="layui-panel">
-
+        <div style="padding: 20px 30px;">
-</div>
 
 
-<div class='layui-row' style="margin-top: 80px; margin-left: 80px">
+            {#            选项#}
+            <div class="layui-tab layui-tab-brief " lay-filter="docDemoTabBrief" style="width: 100%; height: 1000px">
+                <ul class="layui-tab-title">
 
-    <div class='layui-col-md9 layui-form-pane'>
+                    {#                    选项卡#}
-        <fieldset class="layui-elem-field layui-field-title" style="margin-top: 30px;">
+                    <li>pfam</li>
-            <legend>fasta文件</legend>
+                </ul>
-        </fieldset>
+                <div class="layui-tab-content" style="height: 100px;">
-        <div class="layui-btn-container" style="display: inline-block">
+                    <form class="layui-form" action="">
-            <button type="button" class="layui-btn layui-btn-normal" id="select_file">选择文件</button>
+
+                        <div class="layui-form-item">
+
+                            <div class="layui-btn-container">
+
+                                <button type="button" class="layui-btn layui-btn-normal" id="select_pfam">select file
+                                </button>
+
+                            </div>
+                        </div>
+
+
+                        <div class="layui-form-item">
+                            <label class="layui-form-label">clan_overlap</label>
+                            <div class="layui-input-inline">
+                                <input type="text" name="username" id="clan_overlap" placeholder="请输入"
+                                       autocomplete="off" class="layui-input">
+                            </div>
+                        </div>
+
+                        <div class="layui-form-item">
+                            <label class="layui-form-label">align</label>
+                            <div class="layui-input-inline">
+                                <input type="text" name="username" id="align" placeholder="请输入"
+                                       autocomplete="off" class="layui-input">
+                            </div>
+                        </div>
+
+
+                        <div class="layui-form-item">
+                            <label class="layui-form-label">e_seq</label>
+                            <div class="layui-input-inline">
+                                <input type="text" name="username" id="e_seq" placeholder="请输入"
+                                       autocomplete="off" class="layui-input">
+                            </div>
+                        </div>
+
+
+                        <div class="layui-form-item">
+                            <label class="layui-form-label">e_dom</label>
+                            <div class="layui-input-inline">
+                                <input type="text" name="username" id="e_dom" placeholder="请输入"
+                                       autocomplete="off" class="layui-input">
+                            </div>
+                        </div>
+
+
+                        <div class="layui-form-item">
+                            <label class="layui-form-label">b_seq</label>
+                            <div class="layui-input-inline">
+                                <input type="text" name="username" id="b_seq" placeholder="请输入"
+                                       autocomplete="off" class="layui-input">
+                            </div>
+                        </div>
+
+
+                        <div class="layui-form-item">
+                            <label class="layui-form-label">b_dom</label>
+                            <div class="layui-input-inline">
+                                <input type="text" name="username" id="b_dom" placeholder="请输入"
+                                       autocomplete="off" class="layui-input">
+                            </div>
+                        </div>
+
+
+                        <div class="layui-form-item">
+
+                            <div class="layui-btn-container">
+
+                                <div id="down">
+
+                                    <button type="button" class="layui-btn" id="pfam_run">run</button>
+                                    {#                                    <button type="button" class="layui-btn" id="gen_to_fa_down">downlode</button>#}
+                                </div>
+
+                            </div>
+                        </div>
+
+
+                    </form>
+
+                </div>
+            </div>
         </div>
 
+
     </div>
 </div>
+</div>
+
+
+<div class="layui-bg-gray" style="float: left; padding: 30px; width:45%">
+    <div class="layui-panel">
+        <div style="padding: 20px 30px;">
+            <div class="layui-tab layui-tab-brief " lay-filter="docDemoTabBrief" style="width: 100%; height: 1000px">
+                <ul class="layui-tab-title">
+                    <li class="layui-this">function</li>
+                </ul>
+
+                <div class="layui-tab-content">
+                    <div class="layui-tab-item layui-show">
+                        <div style="margin-left: 30px;">
+                            <p style="font-size: 20px">Convert standard gff format files to standard gtf
+                                format</p>
+                        </div>
+                    </div>
+                </div>
+            </div>
 
-<div class='layui-row' style="margin-left:80px; margin-top: 20px">
-    <div class='layui-col-md9'>
-        <fieldset class="layui-elem-field layui-field-title" style="margin-top: 20px;">
-            <legend>运行</legend>
-        </fieldset>
-        <div class="layui-btn-container">
-            <button type="button" class="layui-btn" id="run">RUN</button>
         </div>
     </div>
 </div>
+

tools/urls.py

@@ -6,5 +6,9 @@ urlpatterns = [
     url("(.*\.html$)", views.out_page),
     url("gen_to_fa", views.gen_to_fa),
     url("gff_to_gtf", views.gff_to_gtf),
-    url("blast", views.blast)
+    url("blast", views.blast),
+    url("orf", views.orf),
+    url("basics", views.basics),
+    url("pfam", views.pfam),
+    url("Differential_expression_analysis", views.Differential_expression_analysis)
 ]

tools/views.py

@@ -1,9 +1,10 @@
-import os, time
+import os
 
+from Bio import SeqIO
 from django.http import JsonResponse
 from django.shortcuts import render
+
 from chart import tools
-from Bio import SeqIO
 
 
 def out_page(request, page):
@@ -43,15 +44,6 @@ def gff_to_gtf(request):
     return JsonResponse(data)
 
 
-def gff_to_gtf(request):
-    file = request.FILES.get("file")
-    file_path, file_id = tools.path_out("chart")
-    tools.keep_file(file, file_path)
-    data = {"id": file_id}
-    os.system(f"{tools.tools_path}/gffread {file_path} -T -o {file_path}.gtf")
-    return JsonResponse(data)
-
-
 def orf(request):
     file = request.FILES.get("file", None)
     begin = request.POST.get("begin", None)
@@ -66,3 +58,64 @@ def orf(request):
     os.system(
         f"{tools.tools_path}/ORFfinder {file_path} -b {begin} -e {end} -c {'t' if Cyclotype == 'YES' else 'f'} -g {Codons} -outfmt {outfmt} -out {file_path}.txt")
     return JsonResponse(data)
+
+
+def basics(request):
+    file = request.FILES.get("file", None)
+    # Sequence_cleaning = request.POST.get("Sequence_cleaning", None)  # 序列清洗
+    # Sequence_length = request.POST.get("Sequence_length", None)  # 序列长度
+    # GC_content = request.POST.get("GC_content", None)  # GC含量
+    # Sequence_flip = request.POST.get("Sequence_flip", None)  # 序列翻转
+    # Reverse_complementarity = request.POST.get("Reverse_complementarity", None)  # 反向互补
+    # Codon_preference = request.POST.get("Codon_preference", None)  # 密码子偏好性
+    # Codon_frequency = request.POST.get("Codon_frequency", None)  # 密码子频率
+    file_path, file_id = tools.path_out("chart")
+    tools.keep_file(file, file_path)
+
+    josn = {}
+    for i in request.GET.lists():
+        if i[0] not in ['_', 'file', 'k']:
+            josn[i[0]] = i[1][0]
+
+    data = {"id": file_id}
+
+    tools.Basics(file_path, josn)
+
+    return JsonResponse(data)
+
+
+def pfam(request):
+    file = request.FILES.get("file", None)
+    b_dom = request.POST.get("b_dom", None)
+    b_seq = request.POST.get("b_seq", None)
+    e_dom = request.POST.get("e_dom", None)
+    e_seq = request.POST.get("e_seq", None)
+    align = request.POST.get("align", None)
+    clan_overlap = request.POST.get("clan_overlap", None)
+
+    file_path, file_id = tools.path_out("chart")
+    tools.keep_file(file, file_path)
+    data = {"id": file_id}
+    os.system(
+        f"{tools.tools_path}/pfam_scan.pl -fasta {file_path} -b_dom {b_dom} -b_seq {b_seq} -e_dom {e_dom} -e_seq {e_seq} -align {align} -clan_overlap {clan_overlap} -dir {tools.tools_path}/db/ -out {file_path}.txt")
+
+    return JsonResponse(data)
+
+
+def Differential_expression_analysis(request):
+    if request.method == 'POST':
+        files = request.FILES.getlist('files')
+
+        file_path, file_id = tools.path_out("chart")
+        for f in files:
+            ty = (f.name).split(".")[-1]
+            destination = open('%s/%s' % (file_path, ty), 'wb')
+            for chunk in f.chunks():
+                destination.write(chunk)
+
+            destination.close()
+
+    file_path, file_id = tools.path_out("chart")
+    data = {"id": file_id}
+
+    return JsonResponse(data)