def test_no_aln_possible():
seq1 = 'TTTTTTTTTT'
seq2 = 'AAAAAAAAAAGGG'
pa = PairAlignment(seq1, seq2)
flag, msg = pa.align_with_window([0, 14])
assert not flag
assert 'No alignment found' in msg
def homologous_recombination_proposal(self, cutsite, donor_sequence):
cutsite = cutsite - 1
# check orientation and verify at least 15nt matching on both ends of ODN
if reverse_complement(donor_sequence[:self.__class__.MIN_HOMOLOGY_ARM]
) in self.wt_basecalls:
donor_sequence = reverse_complement(donor_sequence)
if donor_sequence[:self.__class__.MIN_HOMOLOGY_ARM] in self.wt_basecalls and \
donor_sequence[-self.__class__.MIN_HOMOLOGY_ARM:] in self.wt_basecalls:
# todo confirm that cutsite is inside the HDR region
donor_alignment = PairAlignment(self.wt_basecalls, donor_sequence)
donor_alignment.align_ssodn()
proposal_bases, proposal_trace, changed_bases, odn_start_pos = self.recombined_outcome_sequence(
donor_alignment.all_aligned_seqs, donor_sequence)
ep = EditProposal()
ep.sequence_data = proposal_bases
ep.trace_data = proposal_trace
ep.cutsite = cutsite
ep.summary = ProposalBase.HDR
ep.bases_changed = ProposalBase.HDR
return ep, changed_bases, odn_start_pos, donor_alignment
else:
raise Exception(
"Homology arms of length {} not found in control sequence".
format(self.__class__.MIN_HOMOLOGY_ARM))
def test_coord_conversion():
'''
GGGAATGTCCTGATAG
---AATGT--TGATAG
:return:
'''
seq1 = 'GGGAATGTCCTGATAG'
seq2 = 'AATGTTGATAG'
pa = PairAlignment(seq1, seq2)
pa.align_with_window([0,14])
assert 2 == pa.ctrl2sample_coords(5)
assert 0 == pa.ctrl2sample_coords(3)
assert 9 == pa.ctrl2sample_coords(14)
assert None == pa.ctrl2sample_coords(9)
assert 4 == pa.ctrl2sample_coords(9, closest=True)
with pytest.raises(Exception):
pa.ctrl2sample_coords(None)
def no_alignment():
""" returns an example alignment obj """
seq1 = 'AATGTAATGATAG'
seq4 = 'GGACAGACTTAAA'
pa = PairAlignment(seq1, seq4)
return pa
def shorter_alignment():
""" returns an example alignment obj """
seq1 = 'AATGTAATGATAG'
seq3 = 'AATGTATGATAGTGGG'
pa = PairAlignment(seq1, seq3)
return pa
def example_alignment():
""" returns an example alignment obj """
seq1 = 'AATGTAATGATAG'
seq2 = 'AATGTATGATAG'
pa = PairAlignment(seq1, seq2)
return pa
def analyze_sample(self):
self.quality_check()
self.find_targets()
if self.donor_odn:
self.check_recombination()
self.find_alignment_window()
alignment = PairAlignment(self.control_sample.primary_base_calls,
self.edited_sample.primary_base_calls)
self.alignment = alignment
alignment.align_all()
alignment.align_with_window(self.alignment_window)
if alignment.has_alignment:
pass
else:
raise Exception(
"No alignment found between control and edited sample")
# aln_flag, msg = self.align_edited_to_control_sequence()
aln_file = self.base_outputname + "all.txt"
alignment.write_aln(alignment.all_aligned_clustal, to_file=aln_file)
aln_file = self.base_outputname + "windowed.txt"
alignment.write_aln(alignment.aln_clustal, to_file=aln_file)
# write to jsons
aln_json_file = self.base_outputname + "all.json"
alignment.write_json(alignment.all_aligned_seqs, aln_json_file)
aln_json_file = self.base_outputname + "windowed.json"
alignment.write_json(alignment.aln_seqs, aln_json_file)
self._generate_edit_proposals()
if self.donor_odn:
aln_file = self.base_outputname + "donor.txt"
self.donor_alignment.write_aln(
self.donor_alignment.all_aligned_clustal, to_file=aln_file)
aln_json_file = self.base_outputname + "donor.json"
self.donor_alignment.write_json(
self.donor_alignment.all_aligned_seqs, aln_json_file)
print("analyzing {} number of edit proposals".format(
len(self.proposals)))
self._calculate_inference_window()
self._generate_coefficient_matrix()
self._generate_outcomes_vector()
self.analyze_and_rank()
self.calculate_discordance()
self.simple_discordance_algorithm()
# output
indel_file = self.base_outputname + "indel.json"
trace_file = self.base_outputname + "trace.json"
generate_discordance_indel_files(self,
self.results,
to_file=indel_file)
generate_trace_files(self, to_file=trace_file)
write_individual_contribs(self,
to_file=self.base_outputname +
"contribs.txt")
write_contribs_json(self, self.base_outputname + "contribs.json")
if self.allprops:
write_all_proposals_json(
self, self.base_outputname + "allproposals.json")