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Update bug fixes for FGA, D13 and D21 loci #46

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merged 3 commits into from
Nov 1, 2021
+605 −1,147
Merged

Update bug fixes for FGA, D13 and D21 loci #46

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10b3416
initial commit
Nov 1, 2021
015fa64
updated marker tests
Nov 1, 2021
56724eb
updated flanking anno test for new SR config file settigns
Nov 1, 2021
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101 changes: 49 additions & 52 deletions lusSTR/marker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -327,11 +327,11 @@ def annotation(self):
if len(self.uas_sequence) < 110:
bracketed_form = collapse_repeats_by_length(self.uas_sequence, 4)
else:
for m in re.finditer('GGGC', self.uas_sequence):
for m in re.finditer('GGGCTGCCTA', self.uas_sequence):
break_point = m.end()
bracketed_form = (
f'{collapse_repeats_by_length(self.uas_sequence[:break_point], 4)} '
f'{sequence_to_bracketed_form(self.uas_sequence[break_point:], 4, self.repeats)}'
f'{collapse_repeats_by_length(self.uas_sequence[break_point:], 4)}'
)
return bracketed_form

Expand Down Expand Up @@ -715,58 +715,55 @@ def annotation(self):
else:
final = list()
prev = 0
if len(sequence) % 4 == 0:
final_string = collapse_repeats_by_length(sequence, 4)
for m in re.finditer('GGAA', sequence):
if prev == 0 or m.start() == prev:
prev = m.end()
else:
break
first_string = sequence[:prev]
second_string = sequence[prev:]
prev = 0
for m in re.finditer('AAAA', second_string):
prev = m.start()
break
if second_string[prev:(prev+6)] == 'AAAAAA':
third_string = second_string[:prev+2]
fourth_string = second_string[prev+2:]
elif prev == 0:
third_string = second_string[:-6]
fourth_string = second_string[-6:]
else:
for m in re.finditer('GGAA', sequence):
if prev == 0 or m.start() == prev:
prev = m.end()
third_string = second_string[:prev]
fourth_string = second_string[prev:]
final.append(collapse_repeats_by_length(first_string, 4))
final.append(sequence_to_bracketed_form(third_string, 4, self.repeats))
count = 0
tmp = list()
for element in re.split('GAAA', fourth_string):
parts = element.split(',')
for i in parts:
if i == '':
count += 1
else:
break
first_string = sequence[:prev]
second_string = sequence[prev:]
prev = 0
for m in re.finditer('AAAA', second_string):
prev = m.start()
break
if second_string[prev:(prev+6)] == 'AAAAAA':
third_string = second_string[:prev+2]
fourth_string = second_string[prev+2:]
elif prev == 0:
third_string = second_string[:-6]
fourth_string = second_string[-6:]
else:
third_string = second_string[:prev]
fourth_string = second_string[prev:]
final.append(collapse_repeats_by_length(first_string, 4))
final.append(sequence_to_bracketed_form(third_string, 4, self.repeats))
count = 0
tmp = list()
for element in re.split('GAAA', fourth_string):
parts = element.split(',')
for i in parts:
if i == '':
count += 1
if count == 1:
tmp.append('GAAA')
elif count >= 2:
tmp.append('[GAAA]' + str(count))
count = 1
if i == 'AAAAAA':
tmp.append('AA AAAA')
elif len(i) > 4:
for x in split_by_n(i, 4, False):
tmp.append(x)
else:
if count == 1:
tmp.append('GAAA')
elif count >= 2:
tmp.append('[GAAA]' + str(count))
count = 1
if i == 'AAAAAA':
tmp.append('AA AAAA')
elif len(i) > 4:
for x in split_by_n(i, 4, False):
tmp.append(x)
else:
tmp.append(i)
if parts[-1] == '' and count > 2:
tmp.append('[GAAA]' + str(count-1))
elif parts[-1] == '' and count <= 2:
tmp.append('GAAA')
last_string_final = ' '.join(tmp)
final.append(last_string_final)
final_string = ' '.join(final)
tmp.append(i)
if parts[-1] == '' and count > 2:
tmp.append('[GAAA]' + str(count-1))
elif parts[-1] == '' and count <= 2:
tmp.append('GAAA')
last_string_final = ' '.join(tmp)
final.append(last_string_final)
final_string = ' '.join(final)
return re.sub(r' +', ' ', final_string)


Expand Down Expand Up @@ -870,7 +867,7 @@ def annotation(self):
second_string_final = re.sub(' ', '', second_string)
if len(second_string_final) % 4 == 0:
split_second_string = collapse_repeats_by_length(second_string_final, 4)
final_string = f'{first_string} {second_string}'
final_string = f'{first_string} {split_second_string}'
elif len(second_string_final) == 6:
third_string = second_string_final[-6:-4]
fourth_string = second_string_final[-4:]
Expand Down
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