tools

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)