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 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,
})