tools

tools/urls.py

@@ -4,7 +4,7 @@ from tools import views
 
 urlpatterns = [
     url("(.*\.html$)", views.out_page),
-    url("id_transform", views.id_transform),
     url("gen_to_fa", views.gen_to_fa),
+    url("gff_to_gtf", views.gff_to_gtf),
     url("blast", views.blast)
 ]

tools/views.py

@@ -3,7 +3,7 @@ import os, time
 from django.http import JsonResponse
 from django.shortcuts import render
 from chart import tools
-from Bio.SeqRecord import SeqRecord
+from Bio import SeqIO
 
 
 def out_page(request, page):
@@ -18,8 +18,8 @@ def id_transform(request):
         return JsonResponse({})
     return JsonResponse({})
 
-def blast(request):
 
+def blast(request):
     file1 = request.FILES.get('file1', None)
     pass
 
@@ -27,10 +27,42 @@ def blast(request):
 def gen_to_fa(request):
     file = request.FILES.get("file")
     file_path, file_id = tools.path_out("chart")
-    keep_file(file, file_path)
+    tools.keep_file(file, file_path)
     data = {"id": file_id}
-    time.sleep(1)
-    # records = SeqIO.parse(file_path, "genbank")  # 读入
-    # SeqIO.write(records, f"{file_path}", "fasta")  # 写出
-
+    records = SeqIO.parse(file_path, "genbank")  # 读入
+    SeqIO.write(records, f"{file_path}.fasta", "fasta")  # 写出
+    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 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)
+    end = request.POST.get("end", None)
+    Cyclotype = request.POST.get("Cyclotype", None)
+    Codons = request.POST.get("Codons", None)
+    outfmt = request.POST.get("outfmt", 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}/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)