def load_pprs():
pprs = list(SeqIO.parse(os.path.join(utils.TestDir, "Known_PPRs.gb"), "gb",
alphabet=Alphabet.generic_dna))
#apply known binding sites
f = open(os.path.join(utils.TestDir, "known_sites.json"))
sites = json.load(f)
for name,location in sites.iteritems():
for p in pprs:
if p.name.lower() == name.lower():
p.footprints = [l.replace('u','t') for l in location]
#build PSSMs
for p in pprs:
p.barkan = PSSM.build(p, 'barkan')
p.yagi = PSSM.build(p, 'yagi')
p.exact = [build_exact(footprint) for footprint in p.footprints]
return pprs
def load_pprs():
pprs = list(
SeqIO.parse(os.path.join(utils.TestDir, "Known_PPRs.gb"),
"gb",
alphabet=Alphabet.generic_dna))
#apply known binding sites
f = open(os.path.join(utils.TestDir, "known_sites.json"))
sites = json.load(f)
for name, location in sites.iteritems():
for p in pprs:
if p.name.lower() == name.lower():
p.footprints = [l.replace('u', 't') for l in location]
#build PSSMs
for p in pprs:
p.barkan = PSSM.build(p, 'barkan')
p.yagi = PSSM.build(p, 'yagi')
p.exact = [build_exact(footprint) for footprint in p.footprints]
return pprs
def __init__(self, seq_record):
self.seq_record = seq_record
self.pssm = PSSM.build(self.seq_record)
def __init__(self, seq_record):
self.seq_record = seq_record
self.pssm = PSSM.build(self.seq_record)
