def fetch_sequence(request,
feature_type,
stable_id,
stable_id_version,
release_short_name=None,
assembly_name=None,
source_name=None,
seq_type=None,
output_format="fasta"):
if seq_type is not None and seq_type in [
"cds", "five_prime", "three_prime"
]:
sequence_data = TarkSeqUtils.fetch_cds_sequence(
request, feature_type, stable_id, stable_id_version,
release_short_name, assembly_name, source_name, seq_type,
output_format)
else:
sequence_data = TarkSeqUtils.fetch_fasta_sequence(
request, feature_type, stable_id, stable_id_version,
release_short_name, assembly_name, source_name, output_format)
return render(request,
'sequence_fasta.html',
context={
'sequence_data': sequence_data,
'stable_id': stable_id + '.' + stable_id_version,
})
def align_cds_sequence(request,
feature_type,
stable_id_a,
stable_id_version_a,
release_short_name_a,
assembly_name_a,
source_name_a,
stable_id_b,
stable_id_version_b,
release_short_name_b,
assembly_name_b,
source_name_b,
cds_type="cds",
output_format="raw"):
sequence_a = TarkSeqUtils.fetch_cds_sequence(
request, feature_type, stable_id_a, stable_id_version_a,
release_short_name_a, assembly_name_a, source_name_a, cds_type,
output_format)
sequence_b = TarkSeqUtils.fetch_cds_sequence(
request, feature_type, stable_id_b, stable_id_version_b,
release_short_name_b, assembly_name_b, source_name_b, cds_type,
output_format)
if len(sequence_a) == 0 or len(sequence_b) == 0:
return render(
request,
'alignment_viewer.html',
context={
'error_msg':
"Alignment Error...One of the sequence is not available, please check!",
})
pay_load = {
'asequence': sequence_a,
'bsequence': sequence_b,
'format': "pair",
'stype': "dna",
'email': '*****@*****.**'
}
encoded_pay_load = urllib.parse.urlencode(pay_load).encode("utf-8")
# print(encoded_pay_load)
# # #
jobId = TarkSeqUtils.serviceRun(encoded_pay_load)
# jobId = "emboss_needle-R20190607-121522-0390-94599336-p2m"
if jobId:
status = TarkSeqUtils.serviceGetStatus(jobId)
return render(request,
'alignment_viewer.html',
context={
'status': status,
'jobId': jobId,
})
def call_align_sequence_clustal(request):
if request.method == "POST":
data = request.body
body_unicode = data.decode('utf-8')
body = json.loads(body_unicode)
transcript_list = body['payload_data_list']
first_transcript = transcript_list.pop(0)
(first_tr_stable_id, first_tr_stable_id_version
) = first_transcript['transcript1_stable_id'].split('.')
sequence_tr1 = TarkSeqUtils.fetch_fasta_sequence(
request,
"transcript",
first_tr_stable_id,
first_tr_stable_id_version,
release_short_name=first_transcript['transcript1_release'],
assembly_name=first_transcript['transcript1_assembly'],
source_name=first_transcript['transcript1_source'])
output = io.StringIO()
output.write(sequence_tr1)
for transcript in transcript_list:
(tr_stable_id, tr_stable_id_version
) = transcript['transcript2_stable_id'].split('.')
sequence_tr = TarkSeqUtils.fetch_fasta_sequence(
request,
"transcript",
tr_stable_id,
tr_stable_id_version,
release_short_name=transcript['transcript2_release'],
assembly_name=transcript['transcript2_assembly'],
source_name=transcript['transcript2_source'])
print(sequence_tr, file=output, end="")
seq_data = output.getvalue()
pay_load = {
'sequence': seq_data,
'outfmt': 'clustal',
'stype': 'dna',
'email': '*****@*****.**',
'title': "Results from Clustal Multiple Sequence alignment"
}
encoded_pay_load = urllib.parse.urlencode(pay_load).encode("utf-8")
jobId = TarkSeqUtils.serviceRunClustal(encoded_pay_load)
# jobId= "clustalo-R20191210-155816-0727-14316613-p1m"
if jobId:
status = TarkSeqUtils.serviceGetStatus(jobId)
data = {'status': status, 'jobId': jobId}
return JsonResponse(data)
def align_sequence(request,
feature_type,
stable_id_a,
stable_id_version_a,
stable_id_b,
stable_id_version_b,
input_type,
outut_format='pair'):
sequence_a = TarkSeqUtils.fetch_fasta_sequence(request, feature_type,
stable_id_a,
stable_id_version_a)
sequence_b = TarkSeqUtils.fetch_fasta_sequence(request, feature_type,
stable_id_b,
stable_id_version_b)
pay_load = {
'asequence': sequence_a,
'bsequence': sequence_b,
'format': outut_format,
'stype': input_type,
'email': '*****@*****.**'
}
encoded_pay_load = urllib.parse.urlencode(pay_load).encode("utf-8")
# print(encoded_pay_load)
#
jobId = TarkSeqUtils.serviceRun(encoded_pay_load)
# jobId = "emboss_needle-I20190401-145945-0054-27249118-p2m"
if jobId:
status = TarkSeqUtils.serviceGetStatus(jobId)
return render(request,
'alignment_viewer.html',
context={
'status': status,
'jobId': jobId,
})
def align_sequence(query_seq, target_seq):
seq_alignment = TarkSeqUtils.align_sequences(query_seq, target_seq)
return seq_alignment
def format_fasta(sequence, seq_id):
fasta_seq = TarkSeqUtils.format_fasta(sequence, id_=seq_id)
sequence = fasta_seq
return sequence
def check_service_status(request, job_id):
if job_id:
status = TarkSeqUtils.serviceGetStatus(job_id)
return JsonResponse({"status": status})
def test_format_fasta(self):
sequence = "GATTGCGCCACTGCACTCCAGCCTGGGCGTGCAGATCAGAGCGAGACCTTGTCTCTAAAGGAAAAAAAAAAAGAAAGAAAGAAAGAAAAGAAAAGAAAAGAAAACCTAGCGAGGTAGATAATTTT" # @IgnorePep8
formatted_seq = TarkSeqUtils.format_fasta(sequence)
expected_seq = ">ID_\nGATTGCGCCACTGCACTCCAGCCTGGGCGTGCAGATCAGAGCGAGACCTTGTCTCTAAAG\nGAAAAAAAAAAAGAAAGAAAGAAAGAAAAGAAAAGAAAAGAAAACCTAGCGAGGTAGATA\nATTTT\n" # @IgnorePep8
self.assertEqual(formatted_seq, expected_seq, "Sequences are equal")