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utils.py
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utils.py
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def check_rewrite_data(data, data_path):
with open(data_path, 'w') as output_data:
first_is_name = False
need_line = False
seq_num = 0
for x in data:
x = x.strip()
if not x:
continue
if x[0] == '>':
x = adapt_PEPformat(x) # for PEPred-Suite software
seq_num += 1
if need_line:
return False, 'Sorry, sequence ' + str(seq_num - 1) + ' is empty, please check it!'
need_line = True
first_is_name = True
else:
if not first_is_name:
seq_num += 1
return False, 'Sorry, the name of sequence ' + str(seq_num) + ' is wrong, please check it!'
if not is_protein_seq(x):
return False, 'Sorry, sequence ' + str(seq_num) + ' contains wrong alphabet, please check it!'
if not need_line:
seq_num += 1
return False, 'Sorry, the name of sequence ' + str(seq_num) + ' is wrong, please check it!'
need_line = False
output_data.write(x + '\n')
if need_line:
return False, 'Sorry, sequence ' + str(seq_num) + ' is empty, please check it!'
return True, ''
def adapt_PEPformat(x):
"""
PEPred-Suite jar input format
:param x: id that starts with '>'
:return: id that starts with '>' and ends with '|0'
"""
if '|' not in x:
x = x + '|0'
return x
def is_protein_seq(seq):
nchar = ['A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V']
for x in seq:
if x not in nchar:
return False
return True