def view_protein(uuid, protein_id):
hypothesis = get_glycopeptide_hypothesis(uuid)
session = object_session(hypothesis)
protein = session.query(Protein).get(protein_id)
response = render_template("view_glycopeptide_hypothesis/components/protein_view.templ", protein=protein)
session.close()
return response
def handle_glycopeptide_hypothesis(hypothesis):
session = object_session(hypothesis)
protein_table = protein_index(session, hypothesis.id)
response = render_template("view_glycopeptide_hypothesis/container.templ",
hypothesis=hypothesis, protein_table=protein_table)
session.close()
return response
def save_solutions(self, identified_glycopeptides, unassigned_chromatograms,
chromatogram_extractor, database):
if self.analysis_name is None:
return
self.log("Saving Results To \"%s\"" % (self.output_path,))
exporter = self.make_analysis_serializer(
self.output_path,
self.analysis_name,
chromatogram_extractor.peak_loader.sample_run,
identified_glycopeptides,
unassigned_chromatograms,
database,
chromatogram_extractor)
exporter.run()
exporter.set_parameters(
self._build_analysis_saved_parameters(
identified_glycopeptides, unassigned_chromatograms,
chromatogram_extractor, database))
self.analysis = exporter.analysis
self.analysis_id = exporter.analysis.id
for path in self.file_manager.dir():
self.analysis.add_file(path, compress=True)
session = object_session(self.analysis)
session.add(self.analysis)
session.commit()
def paginate_theoretical_glycopeptides(uuid, protein_id, page, per_page=50):
hypothesis = get_glycopeptide_hypothesis(uuid)
session = object_session(hypothesis)
paginator = paginate(session.query(Glycopeptide).filter(
Glycopeptide.protein_id == protein_id), page, per_page)
base_index = (page - 1) * per_page
response = render_template(
"view_glycopeptide_hypothesis/components/display_table.templ",
paginator=paginator, base_index=base_index)
session.close()
return response
def search_glycan_hypothesis(uuid, mass, ppm_tolerance):
hypothesis = get_glycan_hypothesis(uuid)
session = object_session(hypothesis)
lo = mass - (mass * ppm_tolerance)
hi = mass + (mass * ppm_tolerance)
hits = session.query(GlycanComposition).filter(
GlycanComposition.hypothesis_id == hypothesis.id,
GlycanComposition.calculated_mass.between(lo, hi)).all()
converted = [
{"string": hit.composition, "mass": hit.calculated_mass,
"error": (mass - hit.calculated_mass) / hit.calculated_mass} for hit in hits
]
session.close()
if len(converted) == 1:
return jsonify(converted)
else:
return jsonify(*converted)
def view_glycan_composition_hypothesis_table(uuid, page=1):
page_size = 50
hypothesis = get_glycan_hypothesis(uuid)
hypothesis_id = hypothesis.id
def filter_context(q):
return q.filter_by(
hypothesis_id=hypothesis_id)
session = object_session(hypothesis)
paginator = paginate(filter_context(
session.query(GlycanComposition).filter(
GlycanComposition.hypothesis_id == hypothesis_id).order_by(
GlycanComposition.calculated_mass)
), page, page_size)
response = render_template(
"view_glycan_hypothesis/display_table.templ",
paginator=paginator, base_index=(page - 1) * page_size)
session.close()
return response
def view_glycan_composition_hypothesis(uuid):
hypothesis = get_glycan_hypothesis(uuid)
response = render_template("view_glycan_hypothesis/container.templ", hypothesis=hypothesis)
object_session(hypothesis).close()
return response
def handle_glycan_hypothesis(hypothesis):
response = render_template("view_glycan_hypothesis/container.templ", hypothesis=hypothesis)
object_session(hypothesis).close()
return response