def score_chromatograms(self, merged):
chroma_scoring_model = self.peak_shape_scoring_model
scored_merged = []
n = len(merged)
i = 0
for c in merged:
i += 1
if i % 500 == 0:
self.log("%0.2f%% chromatograms evaluated (%d/%d) %r" % (i * 100. / n, i, n, c))
try:
scored_merged.append(ChromatogramSolution(c, scorer=chroma_scoring_model))
except (IndexError, ValueError) as e:
self.log("Could not score chromatogram %r due to %s" % (c, e))
scored_merged.append(ChromatogramSolution(c, score=0.0))
return scored_merged
def evaluate_chromatogram(self, chromatogram):
score_set = self.scoring_model.compute_scores(chromatogram)
score = score_set.product()
return ChromatogramSolution(chromatogram,
score,
scorer=self.scoring_model,
score_set=score_set)
def evaluate_chromatogram(self, chromatogram):
score_set = self.scoring_model.compute_scores(chromatogram)
logitsum_score = score_set.logitsum()
return ChromatogramSolution(chromatogram,
logitsum_score,
scorer=self.scoring_model,
score_set=score_set)
def create(self, structure, chromatogram, shift):
chrom = GlycopeptideChromatogram(structure, ChromatogramTreeList())
chrom = chrom.merge(chromatogram, shift)
# If there is another identification that this wasn't merged with because of varying
# errors in apex time matching, things break down. Check just in case we really want
# to merge here.
try:
existing = self.get_identified_structure_for(structure)
if existing.chromatogram.common_nodes(chrom):
return None
else:
return self.merge(structure, chromatogram, shift)
except KeyError:
pass
ms1_model = self.ms1_scoring_model
chrom = ChromatogramSolution(chrom,
ms1_model.logitscore(chrom),
scorer=ms1_model)
chrom = TandemAnnotatedChromatogram(chrom)
sset = MultiScoreSpectrumSolutionSet(None,
[FakeSpectrumMatch(structure)])
sset.q_value = sset.best_solution().q_value
idgp = IdentifiedGlycopeptide(structure, [sset], chrom)
return idgp
def convert(self, *args, **kwargs):
chromatogram_scoring_model = kwargs.pop(
"chromatogram_scoring_model", GeneralScorer)
chromatogram = self.chromatogram.convert(*args, **kwargs)
composition = self.composition_group.convert() if self.composition_group else None
chromatogram.composition = composition
sol = MemoryChromatogramSolution(
chromatogram, self.score, chromatogram_scoring_model, self.internal_score)
used_as_mass_shift = []
for pair in self.used_as_mass_shift:
used_as_mass_shift.append((pair[0], pair[1].convert()))
sol.used_as_mass_shift = used_as_mass_shift
ambiguous_with = []
for pair in self.ambiguous_with:
ambiguous_with.append((pair[0], pair[1].convert()))
sol.ambiguous_with = ambiguous_with
return sol
def convert(self, *args, **kwargs):
chromatogram_scoring_model = kwargs.pop("chromatogram_scoring_model",
GeneralScorer)
chromatogram = self.chromatogram.convert(*args, **kwargs)
composition = self.composition_group.convert(
) if self.composition_group else None
chromatogram.composition = composition
sol = MemoryChromatogramSolution(chromatogram, self.score,
chromatogram_scoring_model,
self.internal_score)
used_as_adduct = []
for pair in self.used_as_adduct:
used_as_adduct.append((pair[0], pair[1].convert()))
sol.used_as_adduct = used_as_adduct
ambiguous_with = []
for pair in self.ambiguous_with:
ambiguous_with.append((pair[0], pair[1].convert()))
sol.ambiguous_with = ambiguous_with
return sol