Чтение загруженного файла fasta в django с помощью библиотеки Bio
в файле index.html я использовал
<input type="file" name="upload_file">
в файле views.py
from Bio import SeqIO
def index(request):
if request.method == "POST":
try:
text_file = request.FILES['upload_file']
list_1, list_2 = sequence_extract_fasta(text_file)
context = {'files': text_file}
return render(request, 'new.html', context)
except:
text_file = ''
context = {'files': text_file}
return render(request, 'index.html')
def sequence_extract_fasta(fasta_files):
# Defining empty list for the Fasta id and fasta sequence variables
fasta_id = []
fasta_seq = []
# opening a given fasta file using the file path
with open(fasta_files, 'r') as fasta_file:
print("pass")
# extracting multiple data in single fasta file using biopython
for record in SeqIO.parse(fasta_file, 'fasta'): # (file handle, file format)
print(record.seq)
# appending extracted fasta data to empty lists variables
fasta_seq.append(record.seq)
fasta_id.append(record.id)
# returning fasta_id and fasta sequence to both call_compare_fasta and call_reference_fasta
return fasta_id, fasta_seq
Метод sequence_extract_fasta(fasta_files) работает на python. Но не на фреймворке Django. Если я смогу найти временное местоположение загруженного файла, то, используя путь, я смогу вызвать метод. Есть ли какой-нибудь эффективный способ решить эту проблему? Ваша помощь будет высоко оценена. Спасибо за ваше время.
Я нашел один способ сделать это.
def sequence_extract_fasta(fasta_file):
# Defining empty list for the Fasta id and fasta sequence variables
fasta_id = []
fasta_seq = []
# fasta_file = fasta_file.chunks()
print(fasta_file)
# opening given fasta file using the file path
# crating a backup file with original uploaded file data
with open('data/temp/name.bak', 'wb+') as destination:
for chunk in fasta_file.chunks():
destination.write(chunk)
# opening created backup file and reading
with open('data/temp/name.bak', 'r') as fasta_file:
# extracting multiple data in single fasta file using biopython
for record in SeqIO.parse(fasta_file, 'fasta'): # (file handle, file format)
fasta_seq.append(record.seq)
fasta_id.append(record.id)
# returning fasta_id and fasta sequence to both call_compare_fasta and call_reference_fasta
return fasta_id, fasta_seq