def test_analysis_restrictions(self):
"""Test Fancier restriction analysis
"""
new_seq = Seq('TTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA',
IUPACAmbiguousDNA())
rb = RestrictionBatch([EcoRI, KpnI, EcoRV])
ana = Analysis(rb, new_seq, linear=False)
self.assertEqual(
ana.blunt(),
{EcoRV: []}) # output only the result for enzymes which cut blunt
self.assertEqual(ana.full(), {KpnI: [], EcoRV: [], EcoRI: [33]})
self.assertEqual(
ana.with_sites(),
{EcoRI: [33]
}) # output only the result for enzymes which have a site
self.assertEqual(ana.without_site(), {
KpnI: [],
EcoRV: []
}) # output only the enzymes which have no site
self.assertEqual(ana.with_site_size([32]), {})
self.assertEqual(ana.only_between(1, 20),
{}) # the enzymes which cut between position 1 and 20
self.assertEqual(ana.only_between(20, 34), {EcoRI: [33]}) # etc...
self.assertEqual(ana.only_between(34, 20),
{EcoRI: [33]}) # mix start end order
self.assertEqual(ana.only_outside(20, 34), {})
with self.assertWarns(BiopythonWarning):
ana.with_name(['fake'])
self.assertEqual(ana.with_name([EcoRI]), {EcoRI: [33]})
self.assertEqual((ana._boundaries(1, 20)[:2]), (1, 20))
self.assertEqual((ana._boundaries(20, 1)[:2]),
(1, 20)) # reverse order
self.assertEqual((ana._boundaries(-1, 20)[:2]),
(20, 33)) # fix negative start
def enzyme_selector(sequence, restriction_interval, genome_frequency=False, deterministic_overhangs=False, rb=False): """ Usage Example: from utils import extract_feature sequence,_ = extract_feature(sequence_id="AJ627603", data_dir="/home/chymera/data2/gt.ep/sequences/", feature_names=["Cre", "cre", "CRE"]) outp = enzyme_selector(sequence=sequence, restriction_interval=[0,690], genome_frequency=[700,2000], deterministic_overhangs=True) print outp """ from Bio.Restriction import Analysis, AllEnzymes, RestrictionBatch if not rb: basic_analysis = Analysis(AllEnzymes, sequence.seq) else: basic_analysis = Analysis(rb, sequence.seq) respect_target = basic_analysis.only_between(restriction_interval[0],restriction_interval[1]) # print respect_target if genome_frequency: respect_frequency = respect_target for enzyme, item in respect_target.items(): if enzyme.frequency() < genome_frequency[0] or enzyme.frequency() > genome_frequency[1]: del respect_frequency[enzyme] else: if deterministic_overhangs: from utils import overhangs if any(bp_ID in overhangs(enzyme) for bp_ID in ["N", "R", "Y", "!!!", "S", "W", "M", "K", "B", "D", "H", "V"]) or overhangs(enzyme) == "": del respect_frequency[enzyme] return respect_frequency
def test_analysis_restrictions(self):
"""Test Fancier restriction analysis."""
new_seq = Seq('TTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA',
IUPACAmbiguousDNA())
rb = RestrictionBatch([EcoRI, KpnI, EcoRV])
ana = Analysis(rb, new_seq, linear=False)
# Output only the result for enzymes which cut blunt:
self.assertEqual(ana.blunt(), {EcoRV: []})
self.assertEqual(ana.full(), {KpnI: [], EcoRV: [], EcoRI: [33]})
# Output only the result for enzymes which have a site:
self.assertEqual(ana.with_sites(), {EcoRI: [33]})
# Output only the enzymes which have no site:
self.assertEqual(ana.without_site(), {KpnI: [], EcoRV: []})
self.assertEqual(ana.with_site_size([32]), {})
# Output only enzymes which produce 5' overhangs
self.assertEqual(ana.overhang5(), {EcoRI: [33]})
# Output only enzymes which produce 3' overhangs
self.assertEqual(ana.overhang3(), {KpnI: []})
# Output only enzymes which produce defined ends
self.assertEqual(ana.defined(), {KpnI: [], EcoRV: [], EcoRI: [33]})
# Output only enzymes hich cut N times
self.assertEqual(ana.with_N_sites(2), {})
# The enzymes which cut between position x and y:
with self.assertRaises(TypeError):
ana.only_between('t', 20)
with self.assertRaises(TypeError):
ana.only_between(1, 't')
self.assertEqual(ana.only_between(1, 20), {})
self.assertEqual(ana.only_between(20, 34), {EcoRI: [33]})
# Mix start/end order:
self.assertEqual(ana.only_between(34, 20), {EcoRI: [33]})
self.assertEqual(ana.only_outside(20, 34), {})
with self.assertWarns(BiopythonWarning):
ana.with_name(['fake'])
self.assertEqual(ana.with_name([EcoRI]), {EcoRI: [33]})
self.assertEqual((ana._boundaries(1, 20)[:2]), (1, 20))
# Reverse order:
self.assertEqual((ana._boundaries(20, 1)[:2]), (1, 20))
# Fix negative start:
self.assertEqual((ana._boundaries(-1, 20)[:2]), (20, 33))
# Fix negative end:
self.assertEqual((ana._boundaries(1, -1)[:2]), (1, 33))
# Sites in- and outside of boundaries
new_seq = Seq('GAATTCAAAAAAGAATTC', IUPACAmbiguousDNA())
rb = RestrictionBatch([EcoRI])
ana = Analysis(rb, new_seq)
# Cut at least inside
self.assertEqual(ana.between(1, 7), {EcoRI: [2, 14]})
# Cut at least inside and report only inside site
self.assertEqual(ana.show_only_between(1, 7), {EcoRI: [2]})
# Cut at least outside
self.assertEqual(ana.outside(1, 7), {EcoRI: [2, 14]})
# Don't cut within
self.assertEqual(ana.do_not_cut(7, 12), {EcoRI: [2, 14]})
def test_analysis_restrictions(self):
"""Test Fancier restriction analysis."""
new_seq = Seq('TTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA',
IUPACAmbiguousDNA())
rb = RestrictionBatch([EcoRI, KpnI, EcoRV])
ana = Analysis(rb, new_seq, linear=False)
# Output only the result for enzymes which cut blunt:
self.assertEqual(ana.blunt(), {EcoRV: []})
self.assertEqual(ana.full(), {KpnI: [], EcoRV: [], EcoRI: [33]})
# Output only the result for enzymes which have a site:
self.assertEqual(ana.with_sites(), {EcoRI: [33]})
# Output only the enzymes which have no site:
self.assertEqual(ana.without_site(), {KpnI: [], EcoRV: []})
self.assertEqual(ana.with_site_size([32]), {})
# Output only enzymes which produce 5' overhangs
self.assertEqual(ana.overhang5(), {EcoRI: [33]})
# Output only enzymes which produce 3' overhangs
self.assertEqual(ana.overhang3(), {KpnI: []})
# Output only enzymes which produce defined ends
self.assertEqual(ana.defined(), {KpnI: [], EcoRV: [], EcoRI: [33]})
# Output only enzymes hich cut N times
self.assertEqual(ana.with_N_sites(2), {})
# The enzymes which cut between position x and y:
with self.assertRaises(TypeError):
ana.only_between('t', 20)
with self.assertRaises(TypeError):
ana.only_between(1, 't')
self.assertEqual(ana.only_between(1, 20), {})
self.assertEqual(ana.only_between(20, 34), {EcoRI: [33]})
# Mix start/end order:
self.assertEqual(ana.only_between(34, 20), {EcoRI: [33]})
self.assertEqual(ana.only_outside(20, 34), {})
with self.assertWarns(BiopythonWarning):
ana.with_name(['fake'])
self.assertEqual(ana.with_name([EcoRI]), {EcoRI: [33]})
self.assertEqual((ana._boundaries(1, 20)[:2]), (1, 20))
# Reverse order:
self.assertEqual((ana._boundaries(20, 1)[:2]), (1, 20))
# Fix negative start:
self.assertEqual((ana._boundaries(-1, 20)[:2]), (20, 33))
# Fix negative end:
self.assertEqual((ana._boundaries(1, -1)[:2]), (1, 33))
# Sites in- and outside of boundaries
new_seq = Seq('GAATTCAAAAAAGAATTC', IUPACAmbiguousDNA())
rb = RestrictionBatch([EcoRI])
ana = Analysis(rb, new_seq)
# Cut at least inside
self.assertEqual(ana.between(1, 7), {EcoRI: [2, 14]})
# Cut at least inside and report only inside site
self.assertEqual(ana.show_only_between(1, 7), {EcoRI: [2]})
# Cut at least outside
self.assertEqual(ana.outside(1, 7), {EcoRI: [2, 14]})
# Don't cut within
self.assertEqual(ana.do_not_cut(7, 12), {EcoRI: [2, 14]})