def primers():
primers = [
Primer.create(seq="ATGC", fg_freq=1, bg_freq=2, ratio=1.0, active=True),
Primer.create(seq="GGCC", fg_freq=1, bg_freq=3, ratio=0.5, active=True),
Primer.create(seq="CCTA", fg_freq=2, bg_freq=0, ratio=float('inf'), active=True)
]
return primers
def test_create_tables(self):
database.db.init(":memory:")
database.create_tables()
p = Primer.create(seq="ATGC")
s = Set.create(_id=1, score=1)
s.primers.add(p)
database.db.close()
def test_linearize_binding_sites(kmer, initdb, fastafile):
p = Primer.create(seq=kmer)
p._update_locations(fastafile)
chr_ends = swga.locate.chromosome_ends(fastafile)
linear_bind_sites = swga.locate.linearize_binding_sites([p], chr_ends)
# (number of sites + (2*number of chromosomes) - (any overlaps))
assert len(linear_bind_sites) == 10
for record, ends in chr_ends.iteritems():
start, end = ends
assert start in linear_bind_sites
assert end in linear_bind_sites
for site in p.locations()[record]:
assert site in linear_bind_sites
def primers(self, initdb):
primers = [
# reference primer
Primer.create(_id=0, seq="ATGCTC"),
# rev. complement has 4 bases overlapping
Primer.create(_id=1, seq="CAGCAT"),
# rev. complement has 3 bases overlapping
Primer.create(_id=2, seq="GAGGTA"),
Primer.create(_id=3, seq="ATCGAG"),
# rev. complement has one base overlapping
Primer.create(_id=4, seq="TTCCAC"),
# substring of reference primer
Primer.create(_id=5, seq="ATGC")
]
return primers
def tprimers(seqs):
return [Primer.create(seq=seq) for seq in seqs]