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#cython: language_level=3
from obitools3.dms.capi.obitypes cimport is_a_DNA_seq, \
OBI_VOID, \
OBI_BOOL, \
OBI_CHAR, \
OBI_FLOAT, \
OBI_INT, \
OBI_QUAL, \
OBI_SEQ, \
OBI_STR, \
index_t, \
OBI_INT_MAX
from obitools3.dms.capi.obierrno cimport OBI_LINE_IDX_ERROR, \
OBI_ELT_IDX_ERROR, \
obi_errno
from obitools3.files.uncompress cimport CompressedFile
import re
import mmap
import os
import glob
import gzip
cpdef bytes format_uniq_pattern(bytes format):
if format == b"fasta":
return b"\n>"
elif format == b"fastq":
return b"\n\+\n"
elif format == b"ngsfilter" or format == b"tabular":
return b"\n"
elif format == b"genbank" or format == b"embl":
return b"\n//"
elif format == b"ecopcr":
return b"\n[^#]"
else:
return None
cpdef int count_entries(file, bytes format, bint header):
try:
sep = format_uniq_pattern(format)
if sep is None:
return -1
sep = re.compile(sep)
if type(file) == bytes and (format == b'genbank' or format == b'embl'): # file is actually a directory with multiple files
files = []
if format == b'embl':
extensions = [b"*.dat"]
elif format == b"genbank":
extensions = [b"*.gbff"]
for ext in extensions:
for filename in glob.glob(os.path.join(file, ext)):
#if filename[:-3] == ".gz":
# files.append(gzip.open(filename, "rb"))
#else:
files.append(open(filename, "rb"))
else:
files = [file]
if len(files)==0:
return -1
total_count = 0
for f in files:
if type(f) == CompressedFile and f.compressed:
return -1
mmapped_file = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)
total_count += len(re.findall(sep, mmapped_file))
if format != b"ngsfilter" and format != b"tabular" and format != b"embl" and format != b"genbank" and format != b"fastq":
total_count += 1 # adding +1 for 1st entry because separators include \n (ngsfilter and tabular already count one more because of last \n)
if format == b"tabular" and header: # not counting header as an entry
total_count -= 1
except:
if len(files) > 1:
for file in files:
file.close()
return -1
if len(files) > 1:
for f in files:
f.close()
return total_count
# TODO RollbackException?
cdef obi_errno_to_exception(index_t line_nb=-1, object elt_id=None, str error_message=None) :
global obi_errno
if obi_errno > 0 :
if obi_errno == OBI_LINE_IDX_ERROR :
raise IndexError(line_nb, None or error_message)
elif obi_errno == OBI_ELT_IDX_ERROR :
raise IndexError(elt_id, None or error_message)
else :
raise Exception(None or error_message)
cdef bytes str2bytes(str string):
"""
Short cut to convert ascii encoded python string (str) to bytes
which can be easily converted to C-strings.
@param string: the python string to be converted.
@type string: str
@return a transcoded string
@rtype: bytes
"""
return string.encode('ascii')
cdef str bytes2str(bytes string):
"""
Short cut to convert bytes (C-strings) to ascii encoded python string (str).
@param string: the binary (C-string) string to be converted.
@type string: bytes
@return an ascii transcoded string
@rtype: str
"""
return string.decode('ascii')
cdef bytes tobytes(object string):
"""
Short cut to convert ascii encoded string (str or bytes) to bytes
which can be easily converted to C-strings.
@param string: the python string to be converted.
@type string: bytes or str
@return a transcoded string
@rtype: bytes
"""
if string is None:
return None
if isinstance(string, bytes):
return string
return str2bytes(string)
cdef str tostr(object string):
"""
Short cut to convert ascii encoded string (str or bytes) to bytes
which can be easily converted to C-strings.
@param string: the python string to be converted.
@type string: bytes or str
@return a transcoded string
@rtype: bytes
"""
if isinstance(string, str):
return string
return bytes2str(string)
cdef object bytes2str_object(object value): # Only works if complex types are dict or list
if isinstance(value, dict):
items = [(k,v) for k,v in value.items()]
for k, v in items:
if isinstance(v, list) or isinstance(v, dict):
value[k] = bytes2str_object(v)
else:
if type(v) == bytes:
value[k] = bytes2str(v)
if type(k) == bytes:
value[bytes2str(k)] = value.pop(k)
elif isinstance(value, list) or isinstance(value, tuple):
if isinstance(value, tuple):
value = list(value)
for i in range(len(value)):
if isinstance(value[i], list) or isinstance(value[i], dict):
value[i] = bytes2str_object(value[i])
if type(value[i]) == bytes:
value[i] = bytes2str(value[i])
elif type(value) == bytes:
value = bytes2str(value)
return value
cdef object str2bytes_object(object value): # Only works if complex types are dict or list
if isinstance(value, dict):
items = [(k,v) for k,v in value.items()]
for k, v in items:
if isinstance(v, list) or isinstance(v, dict):
value[k] = str2bytes_object(v)
else:
if type(v) == str:
value[k] = str2bytes(v)
if type(k) == str:
value[str2bytes(k)] = value.pop(k)
elif isinstance(value, list):
for i in range(len(value)):
if isinstance(value[i], list) or isinstance(value[i], dict):
value[i] = str2bytes_object(value[i])
if type(value[i]) == str:
value[i] = str2bytes(value[i])
elif type(value) == str:
value = str2bytes(value)
return value
cdef object clean_empty_values_from_object(object value, exclude=[]): # Only works if complex types are dict or list
if isinstance(value, dict):
items = [(k,v) for k,v in value.items()]
for k, v in items:
if isinstance(v, list) or isinstance(v, dict):
value[k] = clean_empty_values_from_object(v)
if (k not in exclude) and (v is None or (hasattr(v, '__len__') and len(v) == 0)):
value.pop(k)
elif isinstance(value, list):
to_remove=[]
for i in range(len(value)):
if isinstance(value[i], list) or isinstance(value[i], dict):
value[i] = clean_empty_values_from_object(value[i])
if value[i] is None or (hasattr(value[i], '__len__') and len(value[i]) == 0):
to_remove.append(value[i])
for v in to_remove:
value.remove(v)
return value
cdef obitype_t get_obitype_single_value(object value) :
cdef type value_type
cdef obitype_t value_obitype
if value is None :
return OBI_VOID
value_type = type(value)
value_obitype = OBI_VOID
if value_type == int :
value_obitype = OBI_INT
elif value_type == float :
value_obitype = OBI_FLOAT
elif value_type == bool :
value_obitype = OBI_BOOL
elif value_type == str or value_type == bytes :
if is_a_DNA_seq(tobytes(value)): #or value_type == Nuc_Seq or value_type == Nuc_Seq_Stored: # TODO discuss
value_obitype = OBI_SEQ
elif len(value) == 1 :
value_obitype = OBI_CHAR
elif (len(value) > 1) :
value_obitype = OBI_STR
else :
value_obitype = OBI_VOID
return value_obitype
cdef obitype_t update_obitype(obitype_t obitype, object new_value) :
cdef type new_type
new_type = type(new_value)
#if new_type == NoneType: # doesn't work because Cython sucks
if new_value == None or new_type==list or new_type==dict or new_type==tuple:
return obitype
# TODO BOOL to INT/FLOAT
if new_type == str or new_type == bytes :
if obitype == OBI_SEQ and is_a_DNA_seq(tobytes(new_value)) :
pass
else :
return OBI_STR
elif obitype == OBI_INT :
if new_type == float or new_value > OBI_INT_MAX :
return OBI_FLOAT
return obitype
cdef obitype_t get_obitype_iterable_value(object value, type t) :
cdef obitype_t value_obitype
value_obitype = OBI_VOID
if t == dict:
for k in value :
if value_obitype == OBI_VOID :
value_obitype = get_obitype_single_value(value[k])
else :
value_obitype = update_obitype(value_obitype, value[k])
elif t == list or t == tuple:
for v in value :
if value_obitype == OBI_VOID :
value_obitype = get_obitype_single_value(v)
else :
value_obitype = update_obitype(value_obitype, v)
return value_obitype
cdef obitype_t get_obitype(object value) :
t = type(value)
if t == dict or t == list or t == tuple :
return get_obitype_iterable_value(value, t)
else :
return get_obitype_single_value(value)
__re_int__ = re.compile(b"^[+-]?[0-9]+$")
__re_float__ = re.compile(b"^[+-]?[0-9]+(\.[0-9]*)?([eE][+-]?[0-9]+)?$")
__re_str__ = re.compile(b"""^"[^"]*"|'[^']*'$""")
__re_dict__ = re.compile(b"""^\{\ *
(
("[^"]*"|'[^']*')
\ *:\ *
([^,}]+|
"[^"]*"|
'[^']*'
)
)?
(\ *,\ *
("[^"]*"|'[^']*')
\ *:\ *
([^,}]+|
"[^"]*"|
'[^']*'
)
)*\ *\}$""", re.VERBOSE)
__re_val__ = re.compile(b"""(("[^"]*"|'[^']*') *: *([^,}]+|"[^"]*"|'[^']*') *[,}] *)""")
cdef object __etag__(bytes x, bytes nastring=b"NA"):
cdef list elements
cdef tuple i
if x == nastring:
v = None
elif __re_int__.match(x):
v=int(x)
elif __re_float__.match(x):
v=float(x)
elif __re_str__.match(x):
v=x[1:-1]
elif x==b'None':
v=None
elif x==b'False':
v=False
elif x==b'True':
v=True
elif __re_dict__.match(x):
elements=__re_val__.findall(x)
v=dict([(i[1][1:-1],__etag__(i[2])) for i in elements])
else:
v=x
return v
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