def protein_page(request):
try:
query = DBSession.query(Protein.name,
Protein.organism,
Protein.description,
Protein.sequence,
Protein.gene_name)
query = query.filter(Protein.name == request.matchdict["protein"])
temp_statistics = query.all()
statistics = json.dumps(temp_statistics)
query = DBSession.query(SpectrumHit.sequence.distinct())
query = query.join(t_spectrum_protein_map)
query = query.join(Protein)
query = query.join(MsRun)
query = query.filter(Protein.name == request.matchdict["protein"])
query = query.filter(SpectrumHit.source_source_id != None)
query = query.filter(MsRun.flag_trash ==0)
sequences = query.all()
# print sequences
sequence_start = list()
sequence_end = list()
for seq in sequences:
pos = temp_statistics[0][3].find(seq[0])
if pos > -1:
sequence_start.append(pos)
sequence_end.append(pos + len(seq[0]))
sequence_start = json.dumps(sequence_start)
sequence_end = json.dumps(sequence_end)
sequences = js_list_creator_dataTables(sequences)
except:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
return {"statistics": statistics,
"protein": request.matchdict["protein"],
"sequence_start": sequence_start, "sequence_end": sequence_end, "sequences": sequences}
def peptide_page(request):
try:
query = DBSession.query(Protein.name.label("protein"), Protein.gene_name.label("gene_name"))
query = query.join(t_spectrum_protein_map)
query = query.join(SpectrumHit)
query = query.filter(SpectrumHit.sequence == request.matchdict["peptide"])
query = query.group_by(Protein.name)
proteins = json.dumps(query.all())
query = DBSession.query(Source.patient_id)
query = query.join(SpectrumHit)
query = query.join(MsRun)
query = query.filter(MsRun.flag_trash ==0)
query = query.filter(SpectrumHit.sequence == request.matchdict["peptide"])
query = query.group_by(Source.patient_id)
sources = js_list_creator_dataTables(query.all())
except:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
return {"proteins": proteins, "sources": sources,
"peptide": request.matchdict["peptide"]}
