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model_id = MODELS[model]["id"]
peaks_version = MODELS[model]["peaks_version"]
# TODO: Check if 30 is good default CE!
# RG: removed `if ce == 0` in get_vector, split up into two functions
colen = 30
if "ce" in data.columns:
try:
colen = int(float(ces[title]))
except:
sys.stderr.write("Could not parse collision energy!\n")
continue
if vector_file:
# get targets
targets = ms2pip_pyx.get_targets(
modpeptide, msms, peaks, float(fragerror), peaks_version
)
psmids.extend([title] * (len(targets[0])))
if "ce" in data.columns:
dvectors.append(
np.array(
ms2pip_pyx.get_vector_ce(
peptide, modpeptide, charge, colen
),
dtype=np.uint16,
)
) # SD: added collision energy
else:
dvectors.append(
np.array(
ms2pip_pyx.get_vector(peptide, modpeptide, charge),
numby,
numall,
explainedby,
explainedall,
float(numby) / (2 * (len(peptide) - 3)),
float(numall) / (18 * (len(peptide) - 3)),
)
)
else:
# Predict the b- and y-ion intensities from the peptide
pepid_buf.append(title)
peplen_buf.append(len(peptide) - 2)
charge_buf.append(charge)
# get/append ion mzs, targets and predictions
targets = ms2pip_pyx.get_targets(
modpeptide, msms, peaks, float(fragerror), peaks_version
)
target_buf.append([np.array(t, dtype=np.float32) for t in targets])
mzs = ms2pip_pyx.get_mzs(modpeptide, peaks_version)
mz_buf.append([np.array(m, dtype=np.float32) for m in mzs])
predictions = ms2pip_pyx.get_predictions(
peptide, modpeptide, charge, model_id, peaks_version, colen
) # SD: added colen
prediction_buf.append(
[np.array(p, dtype=np.float32) for p in predictions]
)
pcount += 1
if (pcount % 500) == 0:
sys.stdout.write("(%i)%i " % (worker_num, pcount))
sys.stdout.flush()