def parse_file_fasta_seqkey(file_fasta, hsh, options):
if options.get('-a') == '':
print_stderr('reading file into hash\n')
_id = ''
seq = ''
running_1 = 0
FASTA = open_or_die2(file_fasta, 'rb')
while True:
l = FASTA.readline().strip()
if not l:
break
m = re.match(r'^>(\S+)', l)
if m:
_id = m.group()
seq = ''
while True:
ll = FASTA.readline().strip()
if not ll:
break
mm = re.match(r'^>(\S+)', ll)
if mm:
cnt = find_cnt(_id)
seq = tr(seq, '[acgtun.]', '[ACGTTNN]')
# ATTR: Performance issue below:
# create_hash_key_chain(hsh, 0, seq)
try:
hsh[seq] = (hsh[seq]) + cnt
except KeyError:
hsh[seq] = cnt
running_1 += 1
if options.get('-a') == '':
print_stderr('{}\r'.format(running_1))
_id = mm.group()
seq = ''
continue
seq += ll
cnt = find_cnt(_id)
seq = tr(seq, '[acgtun.]', '[ACGTTNN]')
create_hash_key_chain(hsh, 0, seq)
hsh[seq] += cnt
running_1 += 1
if options.get('-a') == '':
print_stderr('{}\r'.format(running_1))
FASTA.close()
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 com(sequence):
return tr(sequence, 'acgtuACGTU', 'TGCAATGCAA')
continue
if re.match(r'^\s*$', l):
continue
if novel or known:
l = l.strip()
line = re.split('\t', l)
coord = 'na'
if len(line) > 16 and line[16]:
coord = line[16]
if known:
if float(line[1]) >= thres and float(line[1]) < maxs:
if options.get('-d') == '':
line[seqcol] = tr(line[seqcol], 'uU', 'tT')
if options.get('-p') == '':
m = re.search(r'\|([a-zA-Z0-9_-]*)$', line[0])
if m:
line[0] = m.groups()[0]
OUT.write(">{}\n{}\n".format(line[0],
line[seqcol].upper()))
else:
OUT.write(">{}_{}_x{}_coord:{}_score:{}\n{}\n".format(
line[0], line[9], line[5], coord, line[1],
line[seqcol].upper()))
coord = coord.strip()
try:
IN = open(sys.argv[1], 'rb')
except IOError:
print('cannot open file {}'.format(sys.argv[1]))
sys.exit(-1)
while True:
l = IN.readline()
if not l:
break
line = re.split(r'\t', l)
if line[1] == '-':
line[4] = str_reverse(line[4])
line[4] = tr(line[4], 'ACGTN', 'TGCAN')
gseq = ssplit(line[4].lower())
edit = ssplit('m' * len(line[4]))
mm = 0
if line[7]:
changes = re.split(r',', line[7])
for change in changes:
match = re.search(r'(\d+):(\w+)\>\w+', change)
if match:
match = match.groups()
mm += 1
gseq[int(match[0])] = match[1].lower()
edit[int(match[0])] = 'M'
def parse_file_struct(file_struct):
global db_old
FILE_STRUCT = open_or_die(file_struct, 'rb',
'can not open file {}\n'.format(file_struct))
while True:
line = FILE_STRUCT.readline()
if not line:
break
line = line.strip()
m = re.match(r'^>(\S+)\s*(.*)', line)
if m:
m = m.groups()
_id = m[0]
desc = m[1]
seq = ""
struct = ""
mfe = ""
while True:
line2 = FILE_STRUCT.readline()
if not line2:
break
line2 = line2.strip()
mm = re.match(r'^>(\S+)\s*(.*)', line2)
if mm:
hash_desc[_id] = desc
hash_seq[_id] = seq
hash_struct[_id] = struct
hash_mfe[_id] = mfe
_id = mm.groups()[0]
desc = mm.groups()[1]
seq = ""
struct = ""
mfe = ""
continue
m3 = re.match(r'^\w', line2)
if m3:
line2 = tr(line2, 'uU', 'tT')
seq += line2
m3 = re.search(r'((\.|\(|\))+)', line2)
if m3:
struct += m3.groups()[0]
m3 = re.search(r'\((\s*-\d+\.\d+)\)', line2)
if m3:
mfe = m3.groups()[0]
hash_desc[_id] = desc
hash_seq[_id] = seq
hash_struct[_id] = struct
hash_mfe[_id] = mfe
# print('\n'.join(sorted(hash_struct.values())))
# print('\n'.join(sorted(hash_desc.keys())))
FILE_STRUCT.close()
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)
