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Copy pathTestAnswerKey.py
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127 lines (124 loc) · 6.02 KB
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__author__ = 'Joseph'
def Test_Answer_Key(ref_genome_file, prv_genome_file, ans_key, allowable_range, verbose=False):
ref_genome = ''
prv_genome = ''
bad_ans_list = []
with open(ref_genome_file, 'r') as gen_file:
for line in gen_file:
if line.startswith('>'):
pass
else:
line = line.rstrip('\n')
ref_genome += line
with open(prv_genome_file, 'r') as gen_file:
for line in gen_file:
if line.startswith('>'):
pass
else:
line = line.rstrip('\n')
prv_genome += line
with open(ans_key, 'r') as answers:
type = ''
for line in answers:
if line.startswith('>'):
line = line.strip()
type = line[1:-1]
else:
if type == 'SNP':
ref_allele = line.split(',')[1]
prv_allele = line.split(',')[2]
posn = int(line.split(',')[3])
found = False
for i in range(posn - allowable_range, posn + allowable_range + 1):
if ref_genome[i] == ref_allele:
temp_ref = ref_genome[i-allowable_range:i] + prv_allele + \
ref_genome[i+1:i+allowable_range+1]
for j in range(posn - allowable_range, posn + allowable_range):
temp_prv = prv_genome[j-allowable_range:j+allowable_range+1]
if temp_prv[:allowable_range] == temp_ref[:allowable_range] or \
temp_prv[allowable_range:] == temp_ref[allowable_range:]:
found = True
if not found:
bad_ans_list.append(str(posn) + ',SNP Error,' + ref_allele + ',' + prv_allele)
elif type == 'COPY':
seq = line.split(',')[1]
for posn in line.split(',')[2:]:
posn = int(posn.rstrip())
found = False
for i in range(posn - allowable_range, posn + allowable_range + 1):
if prv_genome[i:i+len(seq)] == seq:
found = True
if not found:
bad_ans_list.append(str(posn) + ',COPY Error,' + seq)
elif type == 'INVERSION':
seq = line.split(',')[1]
posn = int(line.split(',')[2])
found = False
for i in range(posn - allowable_range, posn + allowable_range + 1):
if prv_genome[i:i+len(seq)] == seq[::-1]:
found = True
inverted = True
for i in range(posn - allowable_range, posn + allowable_range + 1):
if prv_genome[i:i+len(seq)] == seq:
inverted = False
if not inverted:
bad_ans_list.append(str(posn) + ',INV not inverted,' + seq)
elif not found:
bad_ans_list.append(str(posn) + ',INV not found,' + seq)
elif type == 'DELETE':
seq = line.split(',')[1]
posn = int(line.split(',')[2])
found = False
for i in range(posn - allowable_range, posn + allowable_range + 1):
for j in range(posn - allowable_range, posn + allowable_range + 1):
if ref_genome[i:i+len(seq)] == seq:
temp_ref = ref_genome[i-2:i] + ref_genome[i+len(seq):i+len(seq)+3]
if prv_genome[j-2:j+3] == temp_ref:
found = True
if not found:
bad_ans_list.append(str(posn) + ',DELETE error,' + seq)
elif type == 'INSERT':
seq = line.split(',')[1]
posn = int(line.split(',')[2])
found = False
for i in range(posn - allowable_range, posn + allowable_range + 1):
if prv_genome[i:i+len(seq)] == seq:
found = True
if not found:
bad_ans_list.append(str(posn) + ',INSERT error,' + seq)
elif type == 'STR':
seq = line.split(',')[1].rstrip()
repeat = int(line.split(',')[2]) / 2
seq = seq * repeat
posn = int(line.split(',')[3])
prv_found = False
ref_found = False
for i in range(posn - 20, posn + 21):
if prv_genome[i:i+len(seq)] == seq:
prv_found = True
for i in range(posn - 20, posn + 21):
if ref_genome[i:i+len(seq)] == seq:
ref_found = True
if not prv_found:
bad_ans_list.append(str(posn) + ',STR not found,' + seq)
#if ref_found:
# bad_ans_list.append(str(posn) + ',STR not modified,' + seq)
if len(bad_ans_list) > 0:
for line in bad_ans_list:
if not verbose:
print line
else:
posn = int(line.split(',')[0])
print 'Error: ' + line.rstrip()
print 'Genomes surrounding position: ' + str(posn)
print '%11s' % 'V'
print 'Ref: ' + ref_genome[posn - 10:posn + 100]
print 'Prv: ' + prv_genome[posn - 10:posn + 100]
print '\n'
def main():
prv_file_path = 'private_genomeE1.txt'
ref_file_path = 'ref_genomeE1.txt'
ans_file_path = 'ans_genomeE1.txt'
Test_Answer_Key(ref_file_path, prv_file_path, ans_file_path, 5, True)
if __name__ == '__main__':
main()