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Fix for old guppy API and mod calling newline bug #27

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merged 3 commits into from
Nov 9, 2023
Merged

Fix for old guppy API and mod calling newline bug #27

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7892d97
Merge pull request #25 from Psy-Fer/main
Psy-Fer Oct 30, 2023
15d28c6
Handle case where sam_record not available
Psy-Fer Oct 30, 2023
046a361
Make it work for older guppy 5.0.11
Psy-Fer Nov 3, 2023
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29 changes: 23 additions & 6 deletions src/buttery_eel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -518,8 +518,11 @@ def submit_read(args, iq, rq, address, config, params, N):
time.sleep(client.throttle)
continue
else:
model_id = ".".join(args.config.split(".")[:-1])
for calls in bcalled:
done += 1
if not isinstance(calls, list):
calls = [calls]
split_reads = False
if len(calls) > 1:
split_reads = True
Expand All @@ -530,7 +533,6 @@ def submit_read(args, iq, rq, address, config, params, N):
# print("{}: {}".format(j, call[i][j]))
# else:
# print("{}: {}".format(i, call[i]))
# sys.exit()
try:
bcalled_read = {}
bcalled_read["sam_record"] = ""
Expand All @@ -542,18 +544,28 @@ def submit_read(args, iq, rq, address, config, params, N):
bcalled_read["read_id"] = read_id
bcalled_read["read_qscore"] = call['metadata']['mean_qscore']
bcalled_read["int_read_qscore"] = int(call['metadata']['mean_qscore'])
bcalled_read["header"] = "@{} parent_read_id={} model_version_id={} mean_qscore={}".format(bcalled_read["read_id"], bcalled_read["parent_read_id"], call['metadata']['model_version_id'], bcalled_read["int_read_qscore"])
bcalled_read["header"] = "@{} parent_read_id={} model_version_id={} mean_qscore={}".format(bcalled_read["read_id"], bcalled_read["parent_read_id"], call['metadata'].get('model_version_id', model_id), bcalled_read["int_read_qscore"])
bcalled_read["sequence"] = call['datasets']['sequence']
except Exception as error:
# handle the exception
print("An exception occurred in stage 1:", type(error).__name__, "-", error)
sys.exit(1)
try:
if len(bcalled_read["sequence"]) == 0:
print("read_id: {} has a sequence length of zero, skipping".format(read_id))
continue
bcalled_read["qscore"] = call['datasets']['qstring']
if args.moves_out:
bcalled_read["move_table"] = call['datasets']['movement']
bcalled_read["model_stride"] = call['metadata']['model_stride']
if args.call_mods:
try:
bcalled_read["sam_record"] = call['metadata']['alignment_sam_record']
except:
# TODO: add warning that mods model not being used, and exit
except Exception as error:
# handle the exception
print("An exception occurred getting sam_record/alignment_sam_record for {}:", read_id, type(error).__name__, "-", error)
bcalled_read["sam_record"] = ""
continue
if args.do_read_splitting:
bcalled_read["num_samples"] = None
bcalled_read["trimmed_samples"] = None
Expand All @@ -564,6 +576,11 @@ def submit_read(args, iq, rq, address, config, params, N):
bcalled_read["num_samples"] = trimmed_duration + bcalled_read["trimmed_samples"]
if bcalled_read["num_samples"] != raw_num_samples:
print("WARNING: {} ns:i:{} != raw_num_samples:{}".format(bcalled_read["read_id"], bcalled_read["num_samples"], raw_num_samples))
except Exception as error:
# handle the exception
print("An exception occurred in stage 2:", type(error).__name__, "-", error)
sys.exit(1)
try:
if SPLIT_PASS:
if bcalled_read["read_qscore"] >= qs_cutoff:
# pass
Expand All @@ -584,7 +601,7 @@ def submit_read(args, iq, rq, address, config, params, N):

# create summary data
if args.seq_sum:
minknow_events = call['metadata']['num_minknow_events']
minknow_events = call['metadata'].get('num_minknow_events', ".")
sample_rate = float(read_store[read_id]["sampling_rate"])
duration = round(float(call['metadata']['duration'] / sample_rate), 6)
num_events = call['metadata']['num_events']
Expand Down Expand Up @@ -621,7 +638,7 @@ def submit_read(args, iq, rq, address, config, params, N):
bcalled_list.append(bcalled_read)
except Exception as error:
# handle the exception
print("An exception occurred:", type(error).__name__, "-", error)
print("An exception occurred in stage 3:", type(error).__name__, "-", error)
sys.exit(1)


Expand Down