def process_taqman_job(job, job_queue, sequence_source, dg_calc):
logger = logging.getLogger(LOGGER_NAME)
struct = JSONMessage.unserialize(job.input_message)
forward_primer_id = struct.forward_primer_id
reverse_primer_id = struct.reverse_primer_id
probe_ids = struct.probe_ids
sequence_group = Session.query(SequenceGroup).get(struct.sequence_group_id)
fp_sequence = Session.query(SequenceGroupComponent).get(forward_primer_id).sequence
rp_sequence = Session.query(SequenceGroupComponent).get(reverse_primer_id).sequence
probes = Session.query(SequenceGroupComponent).filter(SequenceGroupComponent.id.in_(probe_ids)).all()
probe_seqs = [p.sequence for p in probes]
sequences = sequence_source.sequences_for_primers(fp_sequence.sequence, rp_sequence.sequence,
fwd_prefix_length=MAX_CACHE_PADDING,
rev_suffix_length=MAX_CACHE_PADDING)
if sequences is None:
logger.error("Amplicon TaqMan: Could not get response from server [job %s]" % job.id)
job_queue.abort(job, JSONErrorMessage('Could not get response from server.'))
Session.commit()
return
amplicons = create_amplicons_from_pcr_sequences(sequence_group,
forward_primer=fp_sequence,
reverse_primer=rp_sequence,
probes=probe_seqs,
pcr_sequences=sequences)
for amp in amplicons:
populate_amplicon_dgs(amp, dg_calc)
logger.info("Taqman job completed [job %s]" % job.id)
Session.commit()
# TODO: add finish message
# now add SNPs to cached sequences
for amp in amplicons:
for cseq in amp.cached_sequences:
job_queue.add(JOB_ID_PROCESS_SNPS, ProcessSNPMessage(cached_sequence_id=cseq.id),
parent_job=job.parent)
# avoid condition where job completed -- clear child job first
job_queue.finish(job, None)
def process_location_job(job, job_queue, sequence_source, dg_calc):
logger = logging.getLogger(LOGGER_NAME)
struct = JSONMessage.unserialize(job.input_message)
sequence_group = Session.query(SequenceGroup).get(struct.sequence_group_id)
sequence = None
try:
sequence = sequence_source.sequence_around_loc(sequence_group.location_chromosome,
sequence_group.location_base,
sequence_group.amplicon_length,
prefix_length=MAX_CACHE_PADDING,
suffix_length=MAX_CACHE_PADDING)
except Exception:
logger.exception("Could not retrieve sequence for assay location [job %s]: " % job.id)
job_queue.abort(job, JSONErrorMessage('Could not retrieve the sequence for the specified amplicon location.'))
Session.commit()
return
if sequence is None:
logger.error("Amplicon Location: could not get response from server [job %s]: " % job.id)
job_queue.abort(job, JSONErrorMessage('Could not get response from server.'))
Session.commit()
return
amplicons = create_amplicons_from_pcr_sequences(sequence_group,
pcr_sequences=[sequence])
for amp in amplicons:
populate_amplicon_dgs(amp, dg_calc)
logger.info("Location job completed [job %s]" % job.id)
Session.commit()
for amp in amplicons:
for cseq in amp.cached_sequences:
job_queue.add(JOB_ID_PROCESS_SNPS, ProcessSNPMessage(cached_sequence_id=cseq.id),
parent_job=job.parent)
job_queue.finish(job, None)
def process_snp_job(job, job_queue, sequence_source, dg_calc):
logger = logging.getLogger(LOGGER_NAME)
struct = JSONMessage.unserialize(job.input_message)
sequence_group = Session.query(SequenceGroup).get(struct.sequence_group_id)
chromosome = struct.chromosome
snp_start = struct.start
snp_end = struct.end
sequence = None
try:
sequence = sequence_source.sequence_around_region(chromosome, snp_start, snp_end,
sequence_group.amplicon_length,
prefix_length=MAX_CACHE_PADDING,
suffix_length=MAX_CACHE_PADDING)
except Exception:
logger.exception("Could not retrieve sequence around SNP location for [job %s]" % job.id)
job_queue.abort(job, JSONErrorMessage("Could not retrieve sequence around SNP location."))
Session.commit()
return
if sequence is None:
logger.error("Amplicon SNP: could not get response from server [job %s]" % job.id)
job_queue.abort(job, JSONErrorMessage('Could not get response from server.'))
Session.commit()
return
amplicons = create_amplicons_from_pcr_sequences(sequence_group,
pcr_sequences=[sequence])
logger.info("SNP assay job completed [job %s]" % job.id)
Session.commit()
for amp in amplicons:
for cseq in amp.cached_sequences:
job_queue.add(JOB_ID_PROCESS_SNPS, ProcessSNPMessage(cached_sequence_id=cseq.id),
parent_job=job.parent)
job_queue.finish(job, None)
