137 lines
4.3 KiB
Python
137 lines
4.3 KiB
Python
import os
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from Bio import SeqIO
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from django.http import JsonResponse
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from django.shortcuts import render
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from chart import tools
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def out_page(request, page):
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return render(request, f'/tools/{page}')
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def id_transform(request):
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file = request.FILES.get('file', None)
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to = request.POST.get("to", None)
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from_ = request.POST.get("from", None)
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if file is None:
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return JsonResponse({})
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return JsonResponse({})
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def blast(request):
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file1 = request.FILES.get('file1', None)
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pass
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def gen_to_fa(request):
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file = request.FILES.get("file")
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file_path, file_id = tools.path_out("chart")
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tools.keep_file(file, file_path)
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data = {"id": file_id}
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records = SeqIO.parse(file_path, "genbank") # 读入
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SeqIO.write(records, f"{file_path}.fasta", "fasta") # 写出
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return JsonResponse(data)
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def gff_to_gtf(request):
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file = request.FILES.get("file")
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file_path, file_id = tools.path_out("chart")
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tools.keep_file(file, file_path)
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data = {"id": file_id}
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os.system(f"{tools.tools_path}/gffread {file_path} -T -o {file_path}.gtf")
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return JsonResponse(data)
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def orf(request):
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file = request.FILES.get("file", None)
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begin = request.POST.get("begin", None)
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end = request.POST.get("end", None)
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Cyclotype = request.POST.get("Cyclotype", None)
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Codons = request.POST.get("Codons", None)
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outfmt = request.POST.get("outfmt", None)
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file_path, file_id = tools.path_out("chart")
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tools.keep_file(file, file_path)
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data = {"id": file_id}
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os.system(
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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")
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return JsonResponse(data)
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def basics(request):
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file = request.FILES.get("file", None)
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# Sequence_cleaning = request.POST.get("Sequence_cleaning", None) # 序列清洗
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# Sequence_length = request.POST.get("Sequence_length", None) # 序列长度
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# GC_content = request.POST.get("GC_content", None) # GC含量
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# Sequence_flip = request.POST.get("Sequence_flip", None) # 序列翻转
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# Reverse_complementarity = request.POST.get("Reverse_complementarity", None) # 反向互补
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# Codon_preference = request.POST.get("Codon_preference", None) # 密码子偏好性
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# Codon_frequency = request.POST.get("Codon_frequency", None) # 密码子频率
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file_path, file_id = tools.path_out("chart")
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tools.keep_file(file, file_path)
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josn = {}
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for i in request.POST.lists():
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josn[i[0]] = i[1][0]
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print(josn)
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data = {"id": file_id}
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tools.Basics(file_path, josn).run()
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return JsonResponse(data)
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def pfam(request):
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file = request.FILES.get("file", None)
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b_dom = request.POST.get("b_dom", None)
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b_seq = request.POST.get("b_seq", None)
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e_dom = request.POST.get("e_dom", None)
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e_seq = request.POST.get("e_seq", None)
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align = request.POST.get("align", None)
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clan_overlap = request.POST.get("clan_overlap", None)
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file_path, file_id = tools.path_out("chart")
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tools.keep_file(file, file_path)
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data = {"id": file_id}
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os.system(
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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")
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return JsonResponse(data)
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def fastqc(request):
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file = request.FILES.get("file", None)
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format = request.POST.get("format", None)
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if format is None:
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format = "fastq"
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file_path, file_id = tools.path_out("chart")
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tools.keep_file(file, file_path)
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data = {"id": file_id}
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os.mkdir(f"{file_path[:-1]}")
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os.system(
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f"{tools.tools_path}/fastqc -o {file_path[:-1]} -f {format} {file_path}")
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os.system(f"7z a -t7z -r {file_id}.7z {file_path[:-1]}")
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return JsonResponse(data)
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def Differential_expression_analysis(request):
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if request.method == 'POST':
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files = request.FILES.getlist('files')
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file_path, file_id = tools.path_out("chart")
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for f in files:
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ty = (f.name).split(".")[-1]
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destination = open('%s/%s' % (file_path, ty), 'wb')
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for chunk in f.chunks():
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destination.write(chunk)
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destination.close()
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file_path, file_id = tools.path_out("chart")
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data = {"id": file_id}
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return JsonResponse(data)
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