def protein(self, query, mode):
"""Return the Protein object"""
o = ''
p=None
if mode == "GI":
p = Protein.select(Protein.q.gi.contains(query))
elif mode == "Accession":
p = Protein.select(Protein.q.accesion.contains(query))
if p[0].organism == 1:
o = "Drosophila melanogaster"
else:
o = "Saccaromyces cervisiae"
title = "Protein: " + mode + query
return dict(title=title, protein=p[0], organism=o)
def alignment(self, p_gi, a_gi):
"""Return the Alignments object"""
p = Protein.byGi(p_gi)
a = None
for i in p.hits:
if i.alignment_protein.gi == (a_gi):
a = i
if a.query_protein.organism == 1:
q_org = "Drosophila melanogaster"
else:
q_org = "Saccaromyces cervisiae"
if a.alignment_protein.organism == 1:
a_org = "Drosophila melanogaster"
else:
a_org = "Saccaromyces cervisiae"
title = "Alignment: " + a_gi + "and" + p_gi
return dict(title=title, alignment=a, alignment_organism=a_org, query_organism=q_org)
def protein_list(self):
title = "Search Page"
proteins = Protein.select()
count = proteins.count()
return dict(title=title, proteins=proteins, count=count)