def blast(request,
blast_form,
template_init,
template_result,
blast_commandline,
sample_fasta_path,
extra_context=None):
"""
Process blastn/tblastn (blast+) query or set up initial blast form.
"""
if request.method == 'POST':
form = blast_form(request.POST)
if form.is_valid():
query_file_object_tmp = form.cleaned_data['sequence_in_form']
evalue = float(form.cleaned_data['evalue_in_form'])
word_size = int(form.cleaned_data['word_size_in_form'])
database_path = str(form.cleaned_data['blast_db_in_form'])
standard_opt_dic = {
'query': query_file_object_tmp,
'evalue': evalue,
'outfmt': 5,
'db': database_path,
'word_size': word_size
}
annotated = utils.get_annotation(database_path, BLAST_DB_NUCL_LIST)
# none standard options:
try:
matrix = str(form.cleaned_data['matrix_in_form'])
standard_opt_dic["matrix"] = matrix
except:
pass
sensitivity_opt_dic = ast.literal_eval(
str(form.cleaned_data['search_sensitivity_in_form']))
blast_records__file_xml = None
try:
# blast search, parse results from temp file, put them into template for rendering.
blast_records__file_xml, blast_error = utils.run_blast_commands(
blast_commandline,
**dict(standard_opt_dic, **sensitivity_opt_dic))
if len(blast_error) > 0:
return render(request=request,
template_name=template_result,
context={
"blast_record": '',
blast_error: BLAST_CORRECT_PARAMS
})
else:
# converts blast results into objects and pack into list
blast_records_in_object_and_list = utils.blast_records_to_object(
list(NCBIXML.parse(blast_records__file_xml)))
# user defined function to modify blast results
# e.g. join blast results with external database in template
if extra_context is not None:
blast_records_in_object_and_list = extra_context(
blast_records_in_object_and_list)
return render(
request=request,
template_name=template_result,
context={
'application':
blast_records_in_object_and_list[0].application,
'version':
blast_records_in_object_and_list[0].version,
'blast_records': blast_records_in_object_and_list,
'annotated': annotated
})
finally:
# remove result - temporary file
if blast_records__file_xml is not None:
os.remove(blast_records__file_xml.name)
else:
form = blast_form(initial={
'sequence_in_form': '',
'evalue_in_form': EVALUE_BLAST_DEFAULT
})
return render(request=request,
template_name=template_init,
context={
'form':
form,
'sequence_sample_in_fasta':
utils.get_sample_data(sample_fasta_path),
"blast_max_number_seq_in_input":
BLAST_MAX_NUMBER_SEQ_IN_INPUT,
})
def test_get_sample_data(self):
with open(self.fastfile.name) as f:
self.assertEquals(utils.get_sample_data(self.fastfile.name),
f.read())
def test_get_sample_data(self):
with open(self.fastfile.name) as f:
self.assertEquals(utils.get_sample_data(self.fastfile.name), f.read())
def blast(request, blast_form, template_init, template_result, blast_commandline, sample_fasta_path,
extra_context=None):
"""
Process blastn/tblastn (blast+) query or set up initial blast form.
"""
if request.method == 'POST':
form = blast_form(request.POST)
if form.is_valid():
query_file_object_tmp = form.cleaned_data['sequence_in_form']
evalue = float(form.cleaned_data['evalue_in_form'])
word_size = int(form.cleaned_data['word_size_in_form'])
database_path = str(form.cleaned_data['blast_db_in_form'])
standard_opt_dic = {'query': query_file_object_tmp, 'evalue': evalue, 'outfmt': 5, 'db': database_path,
'word_size': word_size}
annotated = utils.get_annotation(database_path, BLAST_DB_NUCL_LIST)
# none standard options:
try:
matrix = str(form.cleaned_data['matrix_in_form'])
standard_opt_dic["matrix"] = matrix
except:
pass
sensitivity_opt_dic = ast.literal_eval(str(form.cleaned_data['search_sensitivity_in_form']))
blast_records__file_xml = None
try:
# blast search, parse results from temp file, put them into template for rendering.
blast_records__file_xml, blast_error = utils.run_blast_commands(blast_commandline,
**dict(standard_opt_dic,
**sensitivity_opt_dic))
if len(blast_error) > 0:
return render(request=request, template_name=template_result,
context={"blast_record": '', blast_error: BLAST_CORRECT_PARAMS})
else:
# converts blast results into objects and pack into list
blast_records_in_object_and_list = utils.blast_records_to_object(
list(NCBIXML.parse(blast_records__file_xml)))
# user defined function to modify blast results
# e.g. join blast results with external database in template
if extra_context is not None:
blast_records_in_object_and_list = extra_context(blast_records_in_object_and_list)
return render(request=request, template_name=template_result,
context={'application': blast_records_in_object_and_list[0].application,
'version': blast_records_in_object_and_list[0].version,
'blast_records': blast_records_in_object_and_list,
'annotated': annotated})
finally:
# remove result - temporary file
if blast_records__file_xml is not None:
os.remove(blast_records__file_xml.name)
else:
form = blast_form(initial={'sequence_in_form': '', 'evalue_in_form': EVALUE_BLAST_DEFAULT})
return render(request=request, template_name=template_init,
context={'form': form, 'sequence_sample_in_fasta': utils.get_sample_data(sample_fasta_path),
"blast_max_number_seq_in_input": BLAST_MAX_NUMBER_SEQ_IN_INPUT, })
