def run_align_aligner(data):
for s in data:
aligner(s[0],
s[1],
method='global',
gap_open=-1,
gap_extend=-1,
matrix=MY_MATRIX)
def test_score(self):
s0 = "AGEBANAN"
s1 = "ACEBAN"
r = aligner(s0,
s1,
gap_extend=-1,
gap_open=-2,
matrix="BLOSUM62",
method=self.method)
assert r == ('AGEBANAN', 'ACEBAN--')
def gen_pic(self): for i, o_w_h in enumerate(self.info, 1): offset, width, height = o_w_h with open(os.path.join(self.path, str(i) + ".bmp"), "wb") as img_out_fh: head_info_obj = add_header.header_info(img_out_fh) head_info_obj.gen_header(width, height) raw = self.data[i-1] if width % 4 == 0: img_out_fh.write(raw) else: align_obj = align.aligner(raw, img_out_fh) align_obj.align_write_raw_data(width, height)
def build_alignments(structure_to_sequences,
pickle_path="./pickled_intermediates"):
''' Given a map, align the canonical and structure-based sequences.
Args:
structure_to_sequences (dict, required. See build_sequence_dict).
'''
alignments = {}
for structure, sequences in structure_to_sequences.items():
print(f"Aligning {structure}...")
fasta_seq = sequences["canonical"].replace("U", "C")
structure_seq = sequences['structure'].replace("U", "C")
alignment = aligner(fasta_seq, structure_seq, method="glocal")[0]
# If there are more than 5 mismatches, there may be a real gap.
# Try a lower gap penalty
if alignment.n_mismatches > 5:
try:
alignment = aligner(fasta_seq,
structure_seq,
method="global",
gap_open=-5,
gap_extend=-1)[0]
except Exception as e:
print(
"[NOTE] An exception is about to raise due to a failed global alignment."
)
print(
f"[NOTE] {structure} had more than 5 mismatches with a semi-global",
f"alignment, but failed to generate any global alignments with gap_open = -5 and gap_extend = -1"
)
raise
alignments[structure] = alignment
print(alignment)
with open(f"{pickle_path}/alignments.pickle", "wb") as f:
pickle.dump(alignments, f)
return alignments
def test_all(self):
r = aligner("CELECANTH", "PELICAN", method=self.method)
assert r == ('CELECANTH', 'PELICAN--'), r
r = aligner("PELICAN", "CELECANTH", method=self.method)
assert r == ('PELICAN--', 'CELECANTH')
def test_it(self):
r = aligner('AAAAAAAAAAAAACCTGCGCCCCAAAAAAAAAAAAAAAAAAAA', 'CCTGCGCACCCC', method='global_cfe')
assert r == ('AAAAAAAAAAAAACCTGCGC-CCCAAAAAAAAAAAAAAAAAAAA', '-------------CCTGCGCACCCC-------------------')
def test_score(self):
s0 = "AGEBANAN"
s1 = "ACEBAN"
r = aligner(s0, s1, gap_extend=-1, gap_open=-2, matrix="BLOSUM62",
method=self.method)
assert r == ('AGEBANAN', 'ACEBAN--')
#!/usr/bin/env python
#-*- coding:utf8 -*-
import add_header
import align
with open('./res/index.txt', 'r') as fh:
lines = fh.readlines()
for i, line in enumerate(lines, 1):
path = './res/'
filename = str(i)
with open(path + filename + '.bmp', 'rb') as img_in_fh:
width, height, offset = line.split()
width, height, offset = int(width), int(height), int(offset)
with open(filename + '.out.bmp', 'wb') as img_out_fh:
head_info_obj = add_header.header_info(img_out_fh)
head_info_obj.gen_header(width, height)
if width % 4 == 0:
raw = img_in_fh.read()
img_out_fh.write(raw)
else:
align_obj = align.aligner(img_in_fh, img_out_fh)
align_obj.align_write(width, height)
def test_all(self):
# global
a, b = aligner('WW', 'WEW', method='global')
assert list(a) == ['W', '-', 'W']
assert list(b) == ['W', 'E', 'W']
a, b = aligner('WW', 'WEW', method='global', gap_open=-100)
assert list(a) == ['W', '-', 'W']
assert list(b) == ['W', 'E', 'W']
a, b = aligner('A', 'A', method='global', gap_open=-7)
assert list(a) == ['A']
assert list(b) == ['A']
a, b = aligner('R', 'K', method='global', gap_open=-7)
assert list(a) == ['R']
assert list(b) == ['K']
a, b = aligner('R', 'AR', method='global', gap_open=-7)
assert list(a) == ['-', 'R'], (a, b)
assert list(b) == ['A', 'R']
a, b = aligner('AR', 'R', method='global', gap_open=-7)
assert list(a) == ['A', 'R']
assert list(b) == ['-', 'R']
a, b = aligner('AR', 'RA', method='global', gap_open=-7)
assert list(a) == ['A', 'R']
assert list(b) == ['R', 'A']
a, b = aligner('AR', 'RA', method='global', gap_open=-3)
assert list(a) == ['A', 'R', '-']
assert list(b) == ['-', 'R', 'A']
a, b = aligner('RAR', 'RR', method='global', gap_open=-3)
assert list(b) == ['R', '-', 'R']
assert list(a) == ['R', 'A', 'R']
a, b = aligner('RAR', 'RR', method='global', gap_open=-10)
assert list(b) == ['R', '-', 'R']
assert list(a) == ['R', 'A', 'R']
a, b = aligner('RAAR', 'RR', method='global', gap_open=-5)
assert list(a) == ['R', 'A', 'A', 'R']
assert list(b) == ['R', '-', '-', 'R']
a, b = aligner('RLR', 'RER', method='global', gap_open=-9)
assert list(a) == ['R', 'L', 'R']
assert list(b) == ['R', 'E', 'R']
a, b = aligner('RLR', 'RER', method='global', gap_open=-1)
assert list(a) == ['R', 'L', '-', 'R']
assert list(b) == ['R', '-', 'E', 'R']
a, b = aligner('RLR', 'REER', method='global', gap_open=-1)
assert list(a) == ['R', 'L', '-', '-', 'R']
assert list(b) == ['R', '-', 'E', 'E', 'R']
a, b = aligner('AGEBAM', 'AGEBAMAM', method='global', gap_open=-6)
assert list(a) == ['A', 'G', 'E', 'B', 'A', 'M', '-', '-']
assert list(b) == ['A', 'G', 'E', 'B', 'A', 'M', 'A', 'M']
a, b = aligner('CPELIRKNCANTH',
'PREKRLICAN',
method='global',
gap_open=-0.5)
assert list(a) == [
'C', 'P', '-', 'E', '-', '-', 'L', 'I', 'R', 'K', 'N', 'C', 'A',
'N', 'T', 'H'
]
assert list(b) == [
'-', 'P', 'R', 'E', 'K', 'R', 'L', 'I', '-', '-', '-', 'C', 'A',
'N', '-', '-'
]
a, b = aligner('CPEL', 'PREK', method='global', gap_open=-6.)
# assert list(a) == ['C', 'P', 'E', 'L']
# assert list(b) == ['P', 'R', 'E', 'K']
a, b = aligner('CPEL', 'PREK', method='global', gap_open=-5)
assert list(a) == ['C', 'P', '-', 'E', 'L']
assert list(b) == ['-', 'P', 'R', 'E', 'K']
a, b = aligner('RLRR', 'RRER', method='global', gap_open=-1)
assert list(a) == ['R', 'L', 'R', '-', 'R']
assert list(b) == ['R', '-', 'R', 'E', 'R']
a, b = aligner('TAAT', 'TAATTC', method='global', matrix='DNA')
assert list(a) == ['T', 'A', 'A', 'T', '-', '-']
assert list(b) == ['T', 'A', 'A', 'T', 'T', 'C']
# global_cfe
a, b = aligner('TAAT', 'TAATTC', method='global_cfe', matrix='DNA')
assert list(a) == ['T', 'A', 'A', 'T', '-', '-']
assert list(b) == ['T', 'A', 'A', 'T', 'T', 'C']
a, b = aligner('TCTAAT', 'TAAT', method='global_cfe', matrix='DNA')
assert list(b) == ['-', '-', 'T', 'A', 'A', 'T']
assert list(a) == ['T', 'C', 'T', 'A', 'A', 'T']
# local
a, b = aligner('TCTAAT', 'TAAT', method='local', matrix='DNA')
assert list(b) == ['T', 'A', 'A', 'T']
assert list(a) == ['T', 'A', 'A', 'T']
a, b = aligner('TCTAAT', 'TAATCT', method='local', matrix='DNA')
assert list(b) == ['T', 'A', 'A', 'T']
assert list(a) == ['T', 'A', 'A', 'T']
# glocal
a, b = aligner('AAATAATAAA', 'TAAT', method='glocal', matrix='DNA')
assert list(b) == ['T', 'A', 'A', 'T']
assert list(a) == ['T', 'A', 'A', 'T']
a, b = aligner('AAATAATAAA',
'TATAT',
method='glocal',
gap_open=-1,
matrix='DNA')
assert list(a) == ['T', 'A', '-', 'A', 'T']
assert list(b) == ['T', 'A', 'T', 'A', 'T']
a, b = aligner('TATATAAA',
'CCTATAT',
method='glocal',
gap_open=-1,
matrix='DNA')
assert (a, b) == ('--TATAT', 'CCTATAT'), (a, b)
a, b = aligner('CCTATAT',
'TATATAAA',
method='glocal',
gap_open=-1,
matrix='DNA')
assert list(b) == ['-', '-', 'T', 'A', 'T', 'A', 'T']
assert list(a) == ['C', 'C', 'T', 'A', 'T', 'A', 'T']
# old
a, b = aligner('A', 'A', method='local')
assert list(a) == ['A']
assert list(b) == ['A']
a, b = aligner('RA', 'AR', method='local')
assert list(a) == ['R']
assert list(b) == ['R']
a, b = aligner('RRR', 'RR', method='local')
assert list(a) == ['R', 'R']
assert list(b) == ['R', 'R']
a, b = aligner('WR', 'WRR', method='global')
assert list(b) == ['W', 'R', 'R']
assert list(a) == ['W', 'R', '-']
a, b = aligner('PYNCHAN', 'YNCH', method='local')
assert list(a) == ['Y', 'N', 'C', 'H']
assert list(b) == ['Y', 'N', 'C', 'H']
a, b = aligner('AIP', 'AP', method='local')
assert list(a) == ['P']
assert list(b) == ['P']
a, b = aligner('AIP', 'AP', method='global')
assert list(a) == ['A', 'I', 'P']
assert list(b) == ['A', '-', 'P']
a, b = aligner('PAA', 'PA', method='local')
assert list(a) == ['P', 'A']
assert list(b) == ['P', 'A']
a, b = aligner('PAA', 'PA', method='global')
assert list(a) == ['P', 'A', 'A']
assert list(b) == ['P', 'A', '-']
a, b = aligner('PAA', 'PA', method='global_cfe')
assert list(a) == ['P', 'A', 'A']
assert list(b) == ['P', 'A', '-']
a, b = aligner('TAATTC',
'TAAT',
method='global',
matrix='DNA',
gap_open=-10,
gap_extend=-1)
assert list(a) == ['T', 'A', 'A', 'T', 'T', 'C']
assert list(b) == ['T', 'A', 'A', 'T', '-', '-']
def test_all(self):
# global
a, b = aligner('WW','WEW', method= 'global')
assert list(a) == ['W', '-', 'W']
assert list(b) == ['W', 'E', 'W']
a, b = aligner('WW','WEW', method= 'global', gap_open=-100)
assert list(a) == ['W', '-', 'W']
assert list(b) == ['W', 'E', 'W']
a,b = aligner('A', 'A', method='global', gap_open=-7)
assert list(a) == ['A']
assert list(b) == ['A']
a,b = aligner('R','K', method='global', gap_open=-7)
assert list(a) == ['R']
assert list(b) == ['K']
a,b = aligner('R','AR', method='global', gap_open=-7)
assert list(a) == ['-','R'], (a, b)
assert list(b) == ['A','R']
a,b = aligner('AR','R', method='global', gap_open=-7)
assert list(a) == ['A','R']
assert list(b) == ['-','R']
a,b = aligner('AR','RA', method='global', gap_open=-7)
assert list(a) == ['A','R']
assert list(b) == ['R','A']
a,b = aligner('AR','RA', method='global', gap_open=-3)
assert list(a) == ['A', 'R', '-']
assert list(b) == ['-', 'R', 'A']
a,b = aligner('RAR','RR', method='global', gap_open=-3)
assert list(b) == ['R', '-', 'R']
assert list(a) == ['R', 'A', 'R']
a,b = aligner('RAR','RR', method='global', gap_open=-10)
assert list(b) == ['R', '-', 'R']
assert list(a) == ['R', 'A', 'R']
a,b = aligner('RAAR','RR', method='global', gap_open=-5)
assert list(a) == ['R', 'A', 'A', 'R']
assert list(b) == ['R', '-', '-', 'R']
a,b = aligner('RLR','RER', method='global', gap_open=-9)
assert list(a) == ['R', 'L', 'R']
assert list(b) == ['R', 'E', 'R']
a,b = aligner('RLR','RER', method='global', gap_open=-1)
assert list(a) == ['R', 'L', '-', 'R']
assert list(b) == ['R', '-', 'E', 'R']
a,b = aligner('RLR','REER', method='global', gap_open=-1)
assert list(a) == ['R', 'L', '-', '-', 'R']
assert list(b) == ['R', '-', 'E', 'E', 'R']
a, b = aligner('AGEBAM', 'AGEBAMAM', method='global', gap_open=-6)
assert list(a) == ['A', 'G', 'E', 'B', 'A', 'M', '-', '-']
assert list(b) == ['A', 'G', 'E', 'B', 'A', 'M', 'A', 'M']
a, b= aligner('CPELIRKNCANTH', 'PREKRLICAN', method='global', gap_open=-0.5)
assert list(a) == ['C', 'P', '-', 'E', '-', '-', 'L', 'I', 'R', 'K', 'N', 'C', 'A', 'N', 'T', 'H']
assert list(b) == ['-', 'P', 'R', 'E', 'K', 'R', 'L', 'I', '-', '-', '-', 'C', 'A', 'N', '-', '-']
a, b= aligner('CPEL', 'PREK', method='global', gap_open=-6.)
# assert list(a) == ['C', 'P', 'E', 'L']
# assert list(b) == ['P', 'R', 'E', 'K']
a, b= aligner('CPEL', 'PREK', method='global', gap_open=-5)
assert list(a) == ['C', 'P', '-','E', 'L']
assert list(b) == ['-','P', 'R', 'E', 'K']
a,b = aligner('RLRR','RRER', method='global', gap_open=-1)
assert list(a) == ['R', 'L', 'R', '-', 'R']
assert list(b) == ['R', '-', 'R', 'E', 'R']
a, b = aligner('TAAT', 'TAATTC', method='global', matrix='DNA')
assert list(a) == ['T', 'A', 'A', 'T', '-', '-']
assert list(b) == ['T', 'A', 'A', 'T', 'T', 'C']
# global_cfe
a, b = aligner('TAAT', 'TAATTC', method='global_cfe', matrix='DNA')
assert list(a) == ['T', 'A', 'A', 'T', '-', '-']
assert list(b) == ['T', 'A', 'A', 'T', 'T', 'C']
a, b = aligner('TCTAAT', 'TAAT', method='global_cfe', matrix='DNA')
assert list(b) == ['-', '-','T', 'A', 'A', 'T' ]
assert list(a) == ['T', 'C','T', 'A', 'A', 'T' ]
# local
a, b = aligner('TCTAAT', 'TAAT', method='local', matrix='DNA')
assert list(b) == ['T', 'A', 'A', 'T' ]
assert list(a) == ['T', 'A', 'A', 'T' ]
a, b = aligner('TCTAAT', 'TAATCT', method='local', matrix='DNA')
assert list(b) == ['T', 'A', 'A', 'T' ]
assert list(a) == ['T', 'A', 'A', 'T' ]
# glocal
a, b = aligner('AAATAATAAA', 'TAAT', method='glocal', matrix='DNA')
assert list(b) == ['T', 'A', 'A', 'T' ]
assert list(a) == ['T', 'A', 'A', 'T' ]
a, b = aligner('AAATAATAAA', 'TATAT', method='glocal', gap_open=-1, matrix='DNA')
assert list(a) == ['T', 'A', '-', 'A', 'T' ]
assert list(b) == ['T', 'A', 'T', 'A', 'T' ]
a, b = aligner('TATATAAA', 'CCTATAT', method='glocal', gap_open=-1, matrix='DNA')
assert (a, b) == ('--TATAT', 'CCTATAT' ), (a, b)
a, b = aligner('CCTATAT', 'TATATAAA',method='glocal', gap_open=-1, matrix='DNA')
assert list(b) == ['-', '-', 'T', 'A', 'T', 'A', 'T' ]
assert list(a) == ['C', 'C', 'T', 'A', 'T', 'A', 'T' ]
# old
a, b = aligner('A', 'A', method ='local')
assert list(a) == ['A']
assert list(b) == ['A']
a, b = aligner('RA', 'AR', method ='local')
assert list(a) == ['R']
assert list(b) == ['R']
a, b = aligner('RRR', 'RR', method ='local')
assert list(a) == ['R', 'R']
assert list(b) == ['R', 'R']
a, b = aligner('WR', 'WRR', method ='global')
assert list(b) == ['W', 'R', 'R']
assert list(a) == ['W', 'R', '-']
a,b = aligner('PYNCHAN', 'YNCH', method='local')
assert list(a) == ['Y', 'N', 'C', 'H']
assert list(b) == ['Y', 'N', 'C', 'H']
a, b = aligner('AIP', 'AP', method='local')
assert list(a) == ['P']
assert list(b) == ['P']
a, b = aligner('AIP', 'AP', method='global')
assert list(a) == ['A','I','P']
assert list(b) == ['A','-','P']
a, b = aligner('PAA', 'PA', method='local')
assert list(a) == ['P','A']
assert list(b) == ['P','A']
a, b = aligner('PAA', 'PA', method='global')
assert list(a) == ['P','A','A']
assert list(b) == ['P','A','-']
a, b = aligner('PAA', 'PA', method='global_cfe')
assert list(a) == ['P','A','A']
assert list(b) == ['P','A','-']
a, b = aligner('TAATTC', 'TAAT', method='global', matrix='DNA', gap_open=-10, gap_extend=-1)
assert list(a) == ['T', 'A', 'A', 'T', 'T', 'C']
assert list(b) == ['T', 'A', 'A', 'T', '-', '-']
def test_all(self):
r = aligner("CELECANTH", "PELICAN", method=self.method)
assert r == ('CELECANTH', 'PELICAN--'), r
r = aligner("PELICAN", "CELECANTH", method=self.method)
assert r == ('PELICAN--', 'CELECANTH')
def test_it(self):
r = aligner('AAAAAAAAAAAAACCTGCGCCCCAAAAAAAAAAAAAAAAAAAA',
'CCTGCGCACCCC',
method='global_cfe')
assert r == ('AAAAAAAAAAAAACCTGCGC-CCCAAAAAAAAAAAAAAAAAAAA',
'-------------CCTGCGCACCCC-------------------')