def excise_position(db_seq, db_lng, excise_beg, excise_end):
excise_beg_limit = max2(1, excise_beg)
excise_end_limit = min2(db_lng, excise_end)
excise_lng = excise_end_limit - excise_beg_limit + 1
excise_seq = substr(db_seq, excise_beg_limit - 1, excise_lng)
return excise_seq
def remove_adapter(_id, seq, prefix):
seq = tr(seq, '[acgtun.]', '[ACGTTNN]')
seq_clipped = None
pattern = r'(\w+)' + prefix
m = re.search(pattern, seq)
if m:
seq_clipped = m.groups()[0]
elif substr(seq, 0, 6) == prefix:
seq_clipped = prefix
else:
finish = 0
while not finish and len(prefix) > 0:
# ATTR: chop $prefix
prefix = prefix[:-1]
mm = re.search(r'(\w+){}$'.format(prefix), seq)
if mm:
seq_clipped = mm.groups()[0]
finish = 1
if not seq_clipped:
seq_clipped = seq
# print ">$id\n$seq_clipped\n";
print('>{}\n{}'.format(_id, seq_clipped))
def make_dir_tmp(pref, MAP):
_today = datetime.datetime.now()
_time = _today.strftime('%d_%m_%y_%H_%M_%S')
MAP.write('\ntimestamp:\t{}\n\n'.format(_time))
num = random.random()
chance = substr(str(num), 2, 10)
_dir = 'dir_mapper{}_{}_{}'.format(pref, chance, _time)
os.mkdir(_dir)
return _dir
def excise_struct(struct, beg, end, strand):
global db_old
lng = len(struct)
# begin can be equal to end if only one nucleotide is excised
if not (beg <= end):
print_stderr(
'begin can not be greater than end for {}\n'.format(db_old))
sys.exit(0)
# rarely, permuted combinations of signature and structure cause out of bound excision errors.
# this happens once appr. every two thousand combinations
if not (beg <= len(struct)):
return 0
# the blast parsed format is 1-indexed, substr is 0-indexed
sub_struct = substr(struct, beg - 1, end - beg + 1)
return sub_struct
def excise_seq(seq, beg, end, strand):
'''
excise sub sequence from the potential precursor
'''
global db_old
# begin can be equal to end if only one nucleotide is excised
if not (beg <= end):
print_stderr('begin can not greater than end for {}\n'.format(db_old))
sys.exit(0)
# rarely, permuted combinations of signature and structure cause out of bound excision errors.
# this happens once appr. every two thousand combinations
if not (beg <= len(seq)):
return 0
# the blast parsed format is 1-indexed, substr is 0-indexed
sub_seq = substr(seq, beg - 1, end - beg + 1)
# if on the minus strand, the reverse complement should be returned
if strand == "-":
sub_seq = revcom(sub_seq)
return sub_seq
if mm:
remove_adapter(_id, seq, prefix)
_id = mm.groups()[0]
seq = ''
continue
seq += ll
remove_adapter(_id, seq, prefix)
FASTA.close()
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('file_fasta')
parser.add_argument('seq_adapter')
if len(sys.argv) != 3:
print(usage)
sys.exit(-1)
args = parser.parse_args(sys.argv[1:3])
file_fasta = args.file_fasta
seq_adapter = args.seq_adapter
seq_test = "TCGTATGCCGTCTTCTGCTTGT"
prefix = substr(seq_adapter, 0, 6)
prefix = tr(prefix, '[acgtun.]', '[ACGTTNN]')
remove_adapters(file_fasta, prefix)
sys.exit(0)