+
+
+
+
+
+
+
+
Convert standard gff format files to standard gtf
+ format
+
+
+
+
-
\ No newline at end of file
+
+
diff --git a/tools/urls.py b/tools/urls.py
index ada5639..49626e2 100644
--- a/tools/urls.py
+++ b/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)
]
diff --git a/tools/views.py b/tools/views.py
index 2407d1e..817ee89 100644
--- a/tools/views.py
+++ b/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)