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# distutils: language = c
# cython: language_level=3
# cython: profile=True
import sys
import time
import logging
import copy
from itertools import chain
from libc.stdlib cimport malloc, free
from libc.string cimport strdup
cimport pyslow5
# Import the Python-level symbols of numpy
import numpy as np
# Import the C-level symbols of numpy
cimport numpy as np
# Numpy must be initialized. When using numpy from C or Cython you must
# _always_ do that, or you will have segfaults
np.import_array()
#
# Class Open for reading and writing slow5/blow5 files
# m attribute sets the read/write state and file extension of p sets the type
#
cdef class Open:
cdef pyslow5.slow5_file_t *s5
cdef pyslow5.slow5_rec_t *rec
cdef pyslow5.slow5_rec_t *read
cdef pyslow5.slow5_rec_t *write
cdef pyslow5.slow5_rec_t **twrite
cdef pyslow5.slow5_rec_t **trec
cdef char **rid
cdef char **rids
cdef pyslow5.uint64_t rids_len
cdef bint index_state
cdef bint header_state
cdef bint header_add_attr_state
cdef bint close_state
cdef pyslow5.uint64_t head_len
cdef pyslow5.uint64_t aux_len
cdef pyslow5.slow5_aux_type *s5_aux_type
cdef int aux_get_err
cdef pyslow5.uint64_t aux_get_len
cdef np.npy_intp shape_get[1]
cdef np.npy_intp shape_seq[1]
cdef char* p
cdef str path
cdef char* m
cdef str mode
cdef str rec_press
cdef str sig_press
cdef int state
cdef int V
cdef object logger
cdef list aux_names
cdef list aux_types
cdef dict error_codes
cdef dict slow5_press_method
cdef pyslow5.int8_t e0
cdef pyslow5.int16_t e1
cdef pyslow5.int32_t e2
cdef pyslow5.int64_t e3
cdef pyslow5.uint8_t e4
cdef pyslow5.uint16_t e5
cdef pyslow5.uint32_t e6
cdef pyslow5.uint64_t e7
cdef pyslow5.float e8
cdef double e9
cdef char e10
cdef int e11
cdef pyslow5.int8_t *e12
cdef pyslow5.int16_t *e13
cdef pyslow5.int32_t *e14
cdef pyslow5.int64_t *e15
cdef pyslow5.uint8_t *e16
cdef pyslow5.uint16_t *e17
cdef pyslow5.uint32_t *e18
cdef pyslow5.uint64_t *e19
cdef float *e20
cdef double *e21
cdef char *e22 # meant to be string, not sure about this
cdef char *channel_number
cdef char *median_before
cdef char *read_number
cdef char *start_mux
cdef char *start_time
cdef char *end_reason # need to add end_reason_val
cdef char *channel_number_val
cdef double median_before_val
cdef pyslow5.int32_t read_number_val
cdef pyslow5.uint8_t start_mux_val
cdef pyslow5.uint64_t start_time_val
cdef char **channel_number_val_array
cdef double *median_before_val_array
cdef pyslow5.int32_t *read_number_val_array
cdef pyslow5.uint8_t *start_mux_val_array
cdef pyslow5.uint64_t *start_time_val_array
cdef pyslow5.float total_time_slow5_get_next
cdef pyslow5.float total_time_yield_reads
cdef pyslow5.float total_single_write_time
cdef pyslow5.float total_multi_write_signal_time
cdef pyslow5.float total_multi_write_time
def __cinit__(self, pathname, mode, rec_press="zlib", sig_press="svb_zd", DEBUG=0):
# Set to default NULL type
self.s5 = NULL
self.rec = NULL
self.read = NULL
self.write = NULL
self.twrite = NULL
self.path = ""
self.p = ""
self.mode = ""
self.m = ""
self.rec_press = ""
self.sig_press = ""
# state for read/write. -1=null, 0=read, 1=write, 2=append
self.state = -1
self.trec = NULL
self.rid = NULL
self.rids = NULL
self.rids_len = 0
self.index_state = False
self.header_state = False
self.header_add_attr_state = False
self.close_state = False
self.s5_aux_type = NULL
self.aux_get_err = 1
self.aux_get_len = 0
self.head_len = 0
self.aux_len = 0
self.shape_seq[0] = 0
self.shape_get[0] = 0
self.e0 = -1
self.e1 = -1
self.e2 = -1
self.e3 = -1
self.e4 = -1
self.e5 = -1
self.e6 = -1
self.e7 = -1
self.e8 = -1.0
self.e9 = -1.0
self.e10 = 0
self.e11 = 0
self.e12 = NULL
self.e13 = NULL
self.e14 = NULL
self.e15 = NULL
self.e16 = NULL
self.e17 = NULL
self.e18 = NULL
self.e19 = NULL
self.e20 = NULL
self.e21 = NULL
self.e22 = NULL
self.channel_number = strdup("channel_number")
self.median_before = strdup("median_before")
self.read_number = strdup("read_number")
self.start_mux = strdup("start_mux")
self.start_time = strdup("start_time")
self.end_reason = strdup("end_reason")
channel_number_val = NULL
median_before_val = -1.0
read_number_val = -1
start_mux_val = -1
start_time_val = -1
channel_number_val_array = NULL
median_before_val_array = NULL
read_number_val_array = NULL
start_mux_val_array = NULL
start_time_val_array = NULL
# cdef something end_reason # some enum
self.total_time_slow5_get_next = 0.0
self.total_time_yield_reads = 0.0
self.total_single_write_time = 0.0
self.total_multi_write_signal_time = 0.0
self.total_multi_write_time = 0.0
# sets up logging level/verbosity
self.V = DEBUG
self.logger = logging.getLogger(__name__)
if self.V == 1:
lev = logging.DEBUG
else:
lev = logging.WARNING
logging.basicConfig(format='%(asctime)s - [%(levelname)s]: %(message)s',
datefmt='%d-%b-%y %H:%M:%S', level=lev)
# This should match slow5_defs.h error codes
self.error_codes = {-1: ["SLOW5_ERR_EOF", "End Of File reached"],
-2: ["SLOW5_ERR_ARG", "bad argument (NULL)"],
-3: ["SLOW5_ERR_TRUNC", "file truncated"],
-4: ["SLOW5_ERR_RECPARSE", "record parsing error"],
-5: ["SLOW5_ERR_IO", "other file I/O error"],
-6: ["SLOW5_ERR_NOIDX", "index not loaded"],
-7: ["SLOW5_ERR_NOTFOUND", "read id not found"],
-8: ["SLOW5_ERR_OTH", "other error (big endian, internal error, etc.)"],
-9: ["SLOW5_ERR_UNK", "file format unknown"],
-10: ["SLOW5_ERR_MEM", "memory (re)allocation error"],
-11: ["SLOW5_ERR_NOAUX", "no auxiliary map"],
-12: ["SLOW5_ERR_NOFLD", "field not found"],
-13: ["SLOW5_ERR_PRESS", "(de)compression failure"],
-14: ["SLOW5_ERR_MAGIC", "magic number invalid"],
-15: ["SLOW5_ERR_VERSION", "version incompatible"],
-16: ["SLOW5_ERR_HDRPARSE", "header parsing error"],
-17: ["SLOW5_ERR_TYPE", "error relating to slow5 type"]}
# slow5_press_method from slow5_press.h
# enum slow5_press_method {
# SLOW5_COMPRESS_NONE,
# SLOW5_COMPRESS_ZLIB,
# SLOW5_COMPRESS_SVB_ZD, /* streamvbyte zigzag delta */
# SLOW5_COMPRESS_ZSTD,
# };
self.slow5_press_method = {"none": 0,
"zlib": 1,
"svb_zd": 2,
"zstd": 3}
p = str.encode(pathname)
self.path = pathname
self.p = strdup(p)
m = str.encode(mode)
self.mode = mode
self.m = strdup(m)
self.logger.debug("FILE: {}, mode: {}".format(self.path, self.mode))
self.logger.debug("FILE: {}, mode: {}".format(self.p, self.m))
# Set state based on mode for file opening
# state for read/write. -1=null, 0=read, 1=write, 2=append
if mode == "r":
self.state = 0
elif mode == "w":
self.state = 1
self.rec_press = rec_press
self.sig_press = sig_press
elif mode == "a":
self.state = 2
else:
self.state = -1
# opens file and creates slow5 object for reading
if self.state == 0:
self.s5 = pyslow5.slow5_open(self.p, self.m)
self.logger.debug("Number of read_groups: {}".format(self.s5.header.num_read_groups))
elif self.state == 1:
self.s5 = pyslow5.slow5_open(self.p, self.m)
if self.s5 is NULL:
self.logger.error("File '{}' could not be opened for writing.".format(self.path))
if "blow5" in self.path.split(".")[-1]:
if self.rec_press in self.slow5_press_method.keys() and self.sig_press in self.slow5_press_method.keys():
ret = pyslow5.slow5_set_press(self.s5, self.slow5_press_method[self.rec_press], self.slow5_press_method[self.sig_press])
if ret != 0:
self.logger.error("slow5_set_press return not 0: {}".format(ret))
raise RuntimeError("Unable to set compression")
else:
self.logger.error("Compression type rec_press: {}, sig_press: {} could not be found.".format(self.rec_press, self.sig_press))
self.logger.error("Please use only the following: {}".format(",".join(press for press in self.slow5_press_method.keys())))
raise KeyError
else:
self.logger.debug("Not writing blow5, skipping compression steps")
elif self.state == 2:
self.s5 = pyslow5.slow5_open(self.p, self.m)
if self.s5 is NULL:
self.logger.error("File '{}' could not be opened for writing - appending.".format(self.path))
else:
self.logger.error("File '{}' unknown open method: {}".format(self.path, self.mode))
# check object was actually created.
if self.s5 is NULL:
raise MemoryError()
def __init__(self, pathname, mode, rec_press="zlib", sig_press="svb_zd", DEBUG=0):
self.aux_names = []
self.aux_types = []
def __dealloc__(self):
if self.p is not NULL:
free(self.p)
if self.m is not NULL:
free(self.m)
if self.rec is not NULL:
slow5_rec_free(self.rec)
if self.read is not NULL:
slow5_rec_free(self.read)
if self.write is not NULL:
slow5_rec_free(self.write)
if self.state in [1, 2]:
if not self.close_state:
if self.s5 is not NULL:
slow5_close(self.s5)
self.close_state = True
self.logger.debug("{} closed".format(self.path))
else:
self.logger.debug("{} already closed".format(self.path))
if self.state == 0:
if not self.close_state:
if self.s5 is not NULL:
slow5_idx_unload(self.s5)
slow5_close(self.s5)
self.close_state = True
self.logger.debug("{} closed".format(self.path))
free(self.channel_number)
free(self.median_before)
free(self.read_number)
free(self.start_mux)
free(self.start_time)
free(self.end_reason)
self.logger.debug("pathname: {}".format(self.path))
self.logger.debug("total_time_slow5_get_next: {} seconds".format(self.total_time_slow5_get_next))
self.logger.debug("total_time_yield_reads: {} seconds".format(self.total_time_yield_reads))
self.logger.debug("total_single_write_time: {} seconds".format(self.total_single_write_time))
self.logger.debug("total_multi_write_signal_time: {} seconds".format(self.total_multi_write_signal_time))
self.logger.debug("total_multi_write_time: {} seconds".format(self.total_multi_write_time))
def _convert_to_pA(self, d):
'''
convert raw signal data to pA using digitisation, offset, and range
float raw_unit = range / digitisation;
for (int32_t j = 0; j < nsample; j++) {
rawptr[j] = (rawptr[j] + offset) * raw_unit;
}
TODO: Use memory view for the loop so it's faster
'''
digitisation = d['digitisation']
range = d['range']
offset = d['offset']
raw_unit = range / digitisation
# new_raw = []
# for i in d['signal']:
# j = (i + offset) * raw_unit
# new_raw.append(float("{0:.2f}".format(round(j,2))))
# new_raw = np.array(raw_unit * (d['signal'] + offset), dtype=np.float32)
new_raw = (raw_unit * (d['signal'] + offset)).astype(np.float32)
return new_raw
# ==========================================================================
# Read SLOW5 file
# ==========================================================================
def _get_read(self, read_id, pA, aux):
'''
read_id = readID of individual read as a string, get's converted to b'str'
pA = Bool for converting signal to picoamps
aux = str 'name'/'all' or list of names of auxiliary fields added to return dictionary
returns dic = dictionary of main fields for read_id, with any aux fields added
'''
if not self.index_state:
self.logger.debug("FILE: {}, mode: {}".format(self.path, self.mode))
# self.logger.debug("FILE: {}, mode: {}".format(self.path, self.m))
self.logger.debug("Creating/loading index...")
ret = slow5_idx_load(self.s5)
if ret != 0:
self.logger.warning("slow5_idx_load return not 0: {}: {}".format(ret, self.error_codes[ret]))
else:
self.index_state = True
dic = {}
aux_dic = {}
ID = str.encode(read_id)
# rec = NULL
ret = slow5_get(ID, &self.rec, self.s5)
if ret != 0:
self.logger.debug("get_read return not 0: {}".format(ret))
return None
# check for aux fields
if aux is not None:
if not self.aux_names or not self.aux_types:
self.aux_names = self.get_aux_names()
self.aux_types = self.get_aux_types()
if type(aux) is str:
# special type 'all'
if aux == "all":
aux_dic = self._get_read_aux(self.aux_names, self.aux_types)
else:
found_single_aux = False
for n, t in zip(self.aux_names, self.aux_types):
if n == aux:
found_single_aux = True
aux_dic = self._get_read_aux([n], [t])
break
if not found_single_aux:
self.logger.warning("get_read unknown aux name: {}".format(aux))
aux_dic.update({aux: None})
elif type(aux) is list:
n_list = []
t_list = []
for n, t in zip(self.aux_names, self.aux_types):
if n in aux:
n_list.append(n)
t_list.append(t)
aux_dic = self._get_read_aux(n_list, t_list)
# Check for items given that did not exist
n_set = set(n_list)
aux_set = set(aux)
if len(aux_set.difference(n_set)) > 0:
for i in aux_set.difference(n_set):
self.logger.warning("get_read unknown aux name: {}".format(i))
aux_dic.update({i: None})
else:
self.logger.debug("get_read aux type unknown, accepts str or list: {}".format(aux))
# get read data
if type(self.rec.read_id) is bytes:
dic['read_id'] = self.rec.read_id.decode()
else:
dic['read_id'] = self.rec.read_id
dic['read_group'] = self.rec.read_group
dic['digitisation'] = self.rec.digitisation
dic['offset'] = self.rec.offset
dic['range'] = self.rec.range
dic['sampling_rate'] = self.rec.sampling_rate
dic['len_raw_signal'] = self.rec.len_raw_signal
# This could be handled by numpy.fromiter() or similar
# Probably MUCH faster
# https://stackoverflow.com/questions/7543675/how-to-convert-pointer-to-c-array-to-python-array
# https://groups.google.com/g/cython-users/c/KnjF7ViaHUM
# dic['signal'] = [self.rec.raw_signal[i] for i in range(self.rec.len_raw_signal)]
# cdef np.npy_intp shape_get[1]
self.shape_get[0] = <np.npy_intp> self.rec.len_raw_signal
signal = copy.deepcopy(np.PyArray_SimpleNewFromData(1, self.shape_get,
np.NPY_INT16, <void *> self.rec.raw_signal))
np.PyArray_UpdateFlags(signal, signal.flags.num | np.NPY_OWNDATA)
dic['signal'] = signal
# if pA=True, convert signal to pA
if pA:
dic['signal'] = self._convert_to_pA(dic)
# if aux data, add to main dic
if aux_dic:
dic.update(aux_dic)
return dic
def _get_batches(self, read_list, size):
"""
batchify readIDs
"""
for i in range(0, len(read_list), size):
yield read_list[i:i+size]
def _get_read_multi(self, read_list, threads, batchsize, pA, aux):
'''
read_list = list of readIDs
pA = Bool for converting signal to picoamps
aux = str 'name'/'all' or list of names of auxiliary fields added to return dictionary
returns dic = dictionary of main fields for read_id, with any aux fields added
threads = how many threads to use to go fast
'''
if not self.index_state:
self.logger.debug("FILE: {}, mode: {}".format(self.path, self.mode))
self.logger.debug("Creating/loading index...")
ret = slow5_idx_load(self.s5)
if ret != 0:
self.logger.warning("slow5_idx_load return not 0: {}: {}".format(ret, self.error_codes[ret]))
else:
self.index_state = True
self.logger.debug("Setting up batching...")
self.logger.debug("read_list: {}".format([i for i in read_list]))
num_reads = len(read_list)
if num_reads > batchsize:
batches = self._get_batches(read_list, size=batchsize)
else:
batches = self._get_batches(read_list, size=num_reads)
self.logger.debug("batch for loop start")
for batch in chain(batches):
self.logger.debug("Batch: {}".format(",".join([i for i in batch])))
batch_len = len(batch)
self.logger.debug("Starting rid assignment")
self.rid = <char **> malloc(sizeof(char*)*batch_len)
for i in range(batch_len):
self.logger.debug("readID: {}, bin: {}".format(batch[i], batch[i].encode()))
self.rid[i] = strdup(batch[i].encode())
self.logger.debug("rid assignment complete")
self.logger.debug("slow5_get_batch: num_reads: {}".format(batch_len))
ret = slow5_get_batch(&self.trec, self.s5, self.rid, batch_len, threads);
self.logger.debug("get_read_multi slow5_get_batch ret: {}".format(ret))
if ret < 0:
self.logger.error("slow5_get_next error code: {}: {}".format(ret, self.error_codes[ret]))
break
if ret == 0:
self.logger.debug("No more reads: {}".format(ret))
break
for i in range(ret):
python_parse_read_start = time.time()
self.rec = self.trec[i]
dic = {}
aux_dic = {}
# check for aux fields
if aux is not None:
if not self.aux_names or not self.aux_types:
self.aux_names = self.get_aux_names()
self.aux_types = self.get_aux_types()
if type(aux) is str:
# special type 'all'
if aux == "all":
aux_dic = self._get_read_aux(self.aux_names, self.aux_types)
else:
found_single_aux = False
for n, t in zip(self.aux_names, self.aux_types):
if n == aux:
found_single_aux = True
aux_dic = self._get_read_aux([n], [t])
break
if not found_single_aux:
self.logger.warning("get_read unknown aux name: {}".format(aux))
aux_dic.update({aux: None})
elif type(aux) is list:
n_list = []
t_list = []
for n, t in zip(self.aux_names, self.aux_types):
if n in aux:
n_list.append(n)
t_list.append(t)
aux_dic = self._get_read_aux(n_list, t_list)
# Check for items given that did not exist
n_set = set(n_list)
aux_set = set(aux)
if len(aux_set.difference(n_set)) > 0:
for i in aux_set.difference(n_set):
self.logger.warning("get_read unknown aux name: {}".format(i))
aux_dic.update({i: None})
else:
self.logger.debug("get_read aux type unknown, accepts str or list: {}".format(aux))
# get read data
if type(self.rec.read_id) is bytes:
dic['read_id'] = self.rec.read_id.decode()
else:
dic['read_id'] = self.rec.read_id
dic['read_group'] = self.rec.read_group
dic['digitisation'] = self.rec.digitisation
dic['offset'] = self.rec.offset
dic['range'] = self.rec.range
dic['sampling_rate'] = self.rec.sampling_rate
dic['len_raw_signal'] = self.rec.len_raw_signal
# This could be handled by numpy.fromiter() or similar
# Probably MUCH faster
# https://stackoverflow.com/questions/7543675/how-to-convert-pointer-to-c-array-to-python-array
# https://groups.google.com/g/cython-users/c/KnjF7ViaHUM
# dic['signal'] = [self.rec.raw_signal[i] for i in range(self.rec.len_raw_signal)]
# cdef np.npy_intp shape_get[1]
self.shape_get[0] = <np.npy_intp> self.rec.len_raw_signal
signal = copy.deepcopy(np.PyArray_SimpleNewFromData(1, self.shape_get,
np.NPY_INT16, <void *> self.rec.raw_signal))
np.PyArray_UpdateFlags(signal, signal.flags.num | np.NPY_OWNDATA)
dic['signal'] = signal
# if pA=True, convert signal to pA
if pA:
dic['signal'] = self._convert_to_pA(dic)
# if aux data, add to main dic
if aux_dic:
dic.update(aux_dic)
yield dic
slow5_free_batch(&self.trec, ret)
for i in range(batch_len):
free(self.rid[i])
free(self.rid)
self.rec = NULL
self.logger.debug("seq_reads_multi timings:")
def _get_read_aux(self, aux_names, aux_types):
'''
get aux field for read
aux_names and aux_types need to be lists, even if a single element
both names and types need to be in the same order, to ensure correct type function is called
This ensures correct C -> python object conversion
Returns dictionary with dic[name] = value
'''
dic = {}
# treat all input as list to simplify
for name, atype in zip(aux_names, aux_types):
a_name = str.encode(name)
if atype == 0:
self.e0 = slow5_aux_get_int8(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e0
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 1:
self.e1 = slow5_aux_get_int16(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e1
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 2:
self.e2 = slow5_aux_get_int32(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e2
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 3:
self.e3 = slow5_aux_get_int64(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e3
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 4:
self.e4 = slow5_aux_get_uint8(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e4
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 5:
self.e5 = slow5_aux_get_uint16(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e5
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 6:
self.e6 = slow5_aux_get_uint32(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e6
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 7:
self.e7 = slow5_aux_get_uint64(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e7
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 8:
self.e8 = slow5_aux_get_float(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e8
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 9:
self.e9 = slow5_aux_get_double(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e9
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 10:
self.e10 = slow5_aux_get_char(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e10
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 11:
self.e11 = slow5_aux_get_enum(self.rec, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e11
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype), self.aux_get_err, self.error_codes[self.aux_get_err])
dic[name] = None
elif atype == 12:
self.e12 = slow5_aux_get_int8_array(self.rec, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e12[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 13:
self.e13 = slow5_aux_get_int16_array(self.rec, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e13[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 14:
self.e14 = slow5_aux_get_int32_array(self.rec, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e14[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 15:
self.e15 = slow5_aux_get_int64_array(self.rec, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e15[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 16:
self.e16 = slow5_aux_get_uint8_array(self.rec, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e16[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 17:
self.e17 = slow5_aux_get_uint16_array(self.rec, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e17[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 18:
self.e18 = slow5_aux_get_uint32_array(self.rec, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e18[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 19:
self.e19 = slow5_aux_get_uint64_array(self.rec, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e19[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 20:
self.e20 = slow5_aux_get_float_array(self.rec, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e20[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 21:
self.e21 = slow5_aux_get_double_array(self.rec, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e21[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 22:
self.e22 = slow5_aux_get_string(self.rec, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
s = ""
for i in range(self.aux_get_len):
l.append(chr(self.e22[i]))
s = "".join(l)
dic[name] = s
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 22:
self.logger.debug("NOT IMPLEMENTED YET: get_aux_types {} self.aux_get_err is {}: {}".format(atype), self.aux_get_err, self.error_codes[self.aux_get_err])
dic[name] = None
else:
self.logger.debug("get_read_aux atype not known, skipping: {}".format(atype))
return dic
def _get_seq_read_aux(self, aux_names, aux_types):
'''
get aux field for read - when doing sequential read, because of separate self.read (vs rec) call
aux_names and aux_types need to be lists, even if a single element
both names and types need to be in the same order, to ensure correct type function is called
This ensures correct C -> python object conversion
Returns dictionary with dic[name] = value
'''
dic = {}
# treat all input as a list to simplify
for name, atype in zip(aux_names, aux_types):
a_name = str.encode(name)
if atype == 0:
self.e0 = slow5_aux_get_int8(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e0
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 1:
self.e1 = slow5_aux_get_int16(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e1
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 2:
self.e2 = slow5_aux_get_int32(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e2
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 3:
self.e3 = slow5_aux_get_int64(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e3
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 4:
self.e4 = slow5_aux_get_uint8(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e4
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 5:
self.e5 = slow5_aux_get_uint16(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e5
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 6:
self.e6 = slow5_aux_get_uint32(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e6
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 7:
self.e7 = slow5_aux_get_uint64(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e7
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 8:
self.e8 = slow5_aux_get_float(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e8
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 9:
self.e9 = slow5_aux_get_double(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e9
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 10:
self.e10 = slow5_aux_get_char(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e10
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 11:
self.e11 = slow5_aux_get_enum(self.read, a_name, &self.aux_get_err)
if self.aux_get_err == 0:
dic[name] = self.e11
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype), self.aux_get_err, self.error_codes[self.aux_get_err])
dic[name] = None
elif atype == 12:
self.e12 = slow5_aux_get_int8_array(self.read, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e12[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 13:
self.e13 = slow5_aux_get_int16_array(self.read, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e13[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 14:
self.e14 = slow5_aux_get_int32_array(self.read, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e14[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 15:
self.e15 = slow5_aux_get_int64_array(self.read, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e15[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 16:
self.e16 = slow5_aux_get_uint8_array(self.read, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e16[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 17:
self.e17 = slow5_aux_get_uint16_array(self.read, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e17[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 18:
self.e18 = slow5_aux_get_uint32_array(self.read, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e18[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 19:
self.e19 = slow5_aux_get_uint64_array(self.read, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e19[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 20:
self.e20 = slow5_aux_get_float_array(self.read, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e20[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 21:
self.e21 = slow5_aux_get_double_array(self.read, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
for i in range(self.aux_get_len):
l.append(self.e21[i])
dic[name] = l
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 22:
self.e22 = slow5_aux_get_string(self.read, a_name, &self.aux_get_len, &self.aux_get_err)
if self.aux_get_err == 0:
l = []
s = ""
for i in range(self.aux_get_len):
l.append(chr(self.e22[i]))
s = "".join(l)
dic[name] = s
else:
self.logger.debug("get_aux_types {} self.aux_get_err is {}: {}".format(atype, self.aux_get_err, self.error_codes[self.aux_get_err]))
dic[name] = None
elif atype == 22:
self.logger.debug("NOT IMPLEMENTED YET: get_aux_types {} self.aux_get_err is {}: {}".format(atype), self.aux_get_err, self.error_codes[self.aux_get_err])
dic[name] = None
else:
self.logger.debug("get_read_aux atype not known, skipping: {}".format(atype))
return dic
def get_read_ids(self):
'''
get all read_ids from index
if no index, build it then get read_ids
No idea why this is needed but whatever
'''
rids = []
if not self.index_state:
self.logger.debug("FILE: {}, mode: {}".format(self.path, self.mode))
# self.logger.debug("FILE: {}, mode: {}".format(self.path, self.m))
self.logger.debug("Creating/loading index...")
ret = slow5_idx_load(self.s5)
if ret != 0:
self.logger.warning("slow5_idx_load return not 0: {}: {}".format(ret, self.error_codes[ret]))
else:
self.index_state = True
self.rids = slow5_get_rids(self.s5, &self.rids_len)
if self.rids_len == 0:
self.logger.error("get_read_ids: length of read_ids is 0, something when wrong")
if self.rids is NULL:
self.logger.error("get_read_ids: returned rids is NULL, something when wrong")
else:
for i in range(self.rids_len):
rids.append(self.rids[i].decode())
rids_len = self.rids_len
return rids, rids_len
def get_read(self, read_id, pA=False, aux=None):
return self._get_read(read_id, pA, aux)
def seq_reads(self, pA=False, aux=None):
'''
returns generator for sequential reading of slow5 file
for pA and aux, see _get_read
'''
aux_dic = {}
row = {}
ret = 0
# While loops check ret of previous read for errors as fail safe
while ret >= 0:
start_slow5_get_next = time.time()
ret = slow5_get_next(&self.read, self.s5)
self.total_time_slow5_get_next = self.total_time_slow5_get_next + (time.time() - start_slow5_get_next)
self.logger.debug("slow5_get_next return: {}".format(ret))
# check for EOF or other errors
if ret < 0:
if ret == -1:
self.logger.debug("slow5_get_next reached end of file (EOF)(-1): {}: {}".format(ret, self.error_codes[ret]))
else:
self.logger.error("slow5_get_next error code: {}: {}".format(ret, self.error_codes[ret]))
break
aux_dic = {}
row = {}
# get aux fields
if aux is not None:
if not self.aux_names or not self.aux_types:
self.aux_names = self.get_aux_names()
self.aux_types = self.get_aux_types()
if type(aux) is str:
if aux == "all":
aux_dic = self._get_seq_read_aux(self.aux_names, self.aux_types)
else:
found_single_aux = False
for n, t in zip(self.aux_names, self.aux_types):
if n == aux:
found_single_aux = True
aux_dic = self._get_seq_read_aux([n], [t])
break
if not found_single_aux:
self.logger.warning("get_read unknown aux name: {}".format(aux))
aux_dic.update({aux: None})
elif type(aux) is list:
n_list = []
t_list = []
for n, t in zip(self.aux_names, self.aux_types):
if n in aux:
n_list.append(n)
t_list.append(t)
aux_dic = self._get_seq_read_aux(n_list, t_list)
# check for items in given list that do not exist
n_set = set(n_list)
aux_set = set(aux)
if len(aux_set.difference(n_set)) > 0:
for i in aux_set.difference(n_set):
self.logger.warning("get_read unknown aux name: {}".format(i))
aux_dic.update({i: None})
else:
self.logger.debug("get_read aux type unknown, accepts str or list: {}".format(aux))
# Get read data
if type(self.read.read_id) is bytes:
row['read_id'] = self.read.read_id.decode()
else:
row['read_id'] = self.read.read_id
row['read_group'] = self.read.read_group
row['digitisation'] = self.read.digitisation
row['offset'] = self.read.offset
row['range'] = self.read.range
row['sampling_rate'] = self.read.sampling_rate
row['len_raw_signal'] = self.read.len_raw_signal
self.shape_seq[0] = <np.npy_intp> self.read.len_raw_signal
signal = copy.deepcopy(np.PyArray_SimpleNewFromData(1, self.shape_seq,
np.NPY_INT16, <void *> self.read.raw_signal))
np.PyArray_UpdateFlags(signal, signal.flags.num | np.NPY_OWNDATA)
row['signal'] = signal
# if pA=True, convert signal to pA
if pA:
row['signal'] = self._convert_to_pA(row)
# if aux data update main dic
if aux_dic:
row.update(aux_dic)
self.total_time_yield_reads = self.total_time_yield_reads + (time.time() - start_slow5_get_next)
yield row
def seq_reads_multi(self, threads=4, batchsize=4096, pA=False, aux=None):
'''
returns generator for sequential reading of slow5 file
for pA and aux, see _get_read
threads: number of threads to use
batchsize: Number of reads to process with thread pool in parallel
'''
aux_dic = {}
row = {}
ret = 1
timedic = {"aux_total_time": 0,
"primary_total_time": 0,
"pA_total_time": 0,
"signal_total_time": 0}
# While loops check ret of previous read for errors as fail safe
while ret > 0:
start_slow5_get_next = time.time()
ret = slow5_get_next_batch(&self.trec, self.s5, batchsize, threads)
self.total_time_slow5_get_next = self.total_time_slow5_get_next + (time.time() - start_slow5_get_next)
self.logger.debug("slow5_get_next_multi return: {}".format(ret))
# check for EOF or other errors
if ret < 0:
if ret == -1:
self.logger.debug("slow5_get_next_multi reached end of file (EOF)(-1): {}: {}".format(ret, self.error_codes[ret]))
else:
self.logger.error("slow5_get_next_multi error code: {}: {}".format(ret, self.error_codes[ret]))
break
for i in range(ret):
python_parse_read_start = time.time()
self.read = self.trec[i]
aux_dic = {}
row = {}
# get aux fields
aux_time_start = time.time()
if aux is not None:
if not self.aux_names or not self.aux_types:
self.aux_names = self.get_aux_names()
self.aux_types = self.get_aux_types()
if type(aux) is str:
if aux == "all":
aux_dic = self._get_seq_read_aux(self.aux_names, self.aux_types)
else:
found_single_aux = False
for n, t in zip(self.aux_names, self.aux_types):
if n == aux:
found_single_aux = True
aux_dic = self._get_seq_read_aux([n], [t])
break
if not found_single_aux:
self.logger.warning("slow5_get_next_multi unknown aux name: {}".format(aux))
aux_dic.update({aux: None})
elif type(aux) is list:
n_list = []
t_list = []
for n, t in zip(self.aux_names, self.aux_types):
if n in aux:
n_list.append(n)
t_list.append(t)
aux_dic = self._get_seq_read_aux(n_list, t_list)
# check for items in given list that do not exist
n_set = set(n_list)
aux_set = set(aux)
if len(aux_set.difference(n_set)) > 0:
for i in aux_set.difference(n_set):
self.logger.warning("slow5_get_next_multi unknown aux name: {}".format(i))
aux_dic.update({i: None})
else:
self.logger.debug("slow5_get_next_multi aux type unknown, accepts str or list: {}".format(aux))
timedic["aux_total_time"] = timedic["aux_total_time"] + (time.time() - aux_time_start)
# Get read data
primary_start_time = time.time()
if type(self.read.read_id) is bytes:
row['read_id'] = self.read.read_id.decode()
else:
row['read_id'] = self.read.read_id
# row['read_id'] = self.read.read_id.decode()
row['read_group'] = self.read.read_group
row['digitisation'] = self.read.digitisation
row['offset'] = self.read.offset
row['range'] = self.read.range
row['sampling_rate'] = self.read.sampling_rate
row['len_raw_signal'] = self.read.len_raw_signal
signal_start_time = time.time()
self.shape_seq[0] = <np.npy_intp> self.read.len_raw_signal
signal = copy.deepcopy(np.PyArray_SimpleNewFromData(1, self.shape_seq,
np.NPY_INT16, <void *> self.read.raw_signal))
np.PyArray_UpdateFlags(signal, signal.flags.num | np.NPY_OWNDATA)
row['signal'] = signal
timedic["signal_total_time"] = timedic["signal_total_time"] + (time.time() - signal_start_time)
timedic["primary_total_time"] = timedic["primary_total_time"] + (time.time() - primary_start_time)
# if pA=True, convert signal to pA
if pA:
pA_start_time = time.time()
row['signal'] = self._convert_to_pA(row)
timedic["pA_total_time"] = timedic["pA_total_time"] + (time.time() - pA_start_time)
# if aux data update main dic
if aux_dic:
row.update(aux_dic)
self.total_time_yield_reads = self.total_time_yield_reads + (time.time() - python_parse_read_start)
yield row
slow5_free_batch(&self.trec, ret)
if ret < batchsize:
self.logger.debug("slow5_get_next_multi has no more batches - batchsize:{} ret:{}".format(batchsize, ret))
break
self.read = NULL
self.logger.debug("seq_reads_multi timings:")
for i in timedic:
self.logger.debug("{}: {}".format(i, timedic[i]))
def get_read_list(self, read_list, pA=False, aux=None):
'''
returns generator for random access of slow5 file
read_list = list of readIDs, if readID not in file, None type returned (need EOF to work)
for pA and aux see _get_read
'''
for r in read_list:
yield self._get_read(r, pA, aux)
def get_read_list_multi(self, read_list, threads=4, batchsize=100, pA=False, aux=None):
'''
returns generator for random access of slow5 file
read_list = list of readIDs, if readID not in file, None type returned (need EOF to work)
for pA and aux see _get_read
threads = number of threads to use to do batched random access
'''
for r in self._get_read_multi(read_list, threads, batchsize, pA, aux):
yield r
def get_header_names(self):
'''
get all header names and return list
'''
headers = []
ret = slow5_get_hdr_keys(self.s5.header, &self.head_len)
self.logger.debug("slow5_get_hdr_keys head_len: {}".format(self.head_len))
if ret == NULL:
self.logger.debug("slow5_get_hdr_keys ret is NULL")
return headers
headers = [ret[i].decode() for i in range(self.head_len)]
free(ret)
return headers
def get_header_value(self, attr, read_group=0):
'''
get header attribute value
'''
a = str.encode(attr)
ret = ''
ret = slow5_hdr_get(a, read_group, self.s5.header).decode()
if not ret:
self.logger.warning("get_header_value header value not found: {} - rg: {}".format(attr, read_group))
return None
return ret
def get_all_headers(self, read_group=0):
'''
get all headers present and return dictionary
'''
dic = {}
headers = self.get_header_names()
for header in headers:
val = self.get_header_value(header, read_group=read_group)
dic[header] = val
return dic
def get_aux_names(self):
'''
get all aux field names, returns list
'''
self.logger.debug("get_aux_names starting")
aux_names = []
ret = slow5_get_aux_names(self.s5.header, &self.aux_len)
self.logger.debug("get_aux_names aux_len: {}".format(self.aux_len))
if ret == NULL:
self.logger.warning("get_aux_names ret is NULL")
return aux_names
aux_names = [ret[i].decode() for i in range(self.aux_len)]
return aux_names
def get_aux_types(self):
'''
get aux attribute type
'''
self.logger.debug("get_aux_types starting")
aux_types = []
self.s5_aux_type = slow5_get_aux_types(self.s5.header, &self.aux_len)
self.logger.debug("get_aux_types aux_len: {}".format(self.aux_len))
if self.s5_aux_type == NULL:
self.logger.warning("get_aux_types self.s5_aux_type is NULL")
return aux_types
aux_types = [self.s5_aux_type[i] for i in range(self.aux_len)]
return aux_types
# ==========================================================================
# Write SLOW5 file
# ==========================================================================
def get_empty_header(self):
'''
returns example empty header dic for user to populate
Any values not populated will be skipped
'''
header = {"asic_id": None,
"asic_id_eeprom": None,
"asic_temp": None,
"asic_version": None,
"auto_update": None,
"auto_update_source": None,
"barcoding_enabled": None,
"bream_is_standard": None,
"configuration_version": None,
"device_id": None,
"device_type": None,
"distribution_status": None,
"distribution_version": None,
"exp_script_name": None,
"exp_script_purpose": None,
"exp_start_time": None,
"experiment_duration_set": None,
"flow_cell_id": None,
"flow_cell_product_code": None,
"guppy_version": None,
"heatsink_temp": None,
"hostname": None,
"installation_type": None,
"local_basecalling": None,
"operating_system": None,
"package": None,
"protocol_group_id": None,
"protocol_run_id": None,
"protocol_start_time": None,
"protocols_version": None,
"run_id": None,
"sample_frequency": None,
"sample_id": None,
"sequencing_kit": None,
"usb_config": None,
"version": None,
"hublett_board_id": None,
"satellite_firmware_version": None}
return header
def get_empty_record(self, aux=False):
'''
Return a dictionary of empty record and types
if axu=True, a second dictionary will be returned with optional aux record
'''
record = {"read_id": None,
"read_group": 0,
"digitisation": None,
"offset": None,
"range": None,
"sampling_rate": None,
"len_raw_signal": None,
"signal": None}
aux_rec = {"channel_number": None,
"median_before": None,
"read_number": None,
"start_mux": None,
"start_time": None}
if aux:
return record, aux_rec
return record
def _header_type_validation(self, header):
'''
internal function to validate header types before pushing to C side
'''
for h in header:
if header[h] is not None:
t = type(header[h])
if t is not type("string"):
self.logger.warning("_header_type_validation {}: {} is not a string type, attempting to convert".format(h, header[h]))
#try and convert
try:
s = str(header[h])
header[h] = s
self.logger.warning("_header_type_validation {}: {} conversion successful".format(h, s))
except:
self.logger.error("_header_type_validation {}: {} could not convert value to string".format(h, header[h]))
raise
return header
def _aux_header_type_validation(self, user_aux_types):
'''
internal function to validate and convert aux types before pushing to C side
'''
slow5_aux_types = {}
py_aux_types = {"channel_number": type("string"),
"median_before": type(1.0),
"read_number": type(10),
"start_mux": type(1),
"start_time": type(100),
"end_reason": None}
C_aux_types = {"channel_number": SLOW5_STRING,
"median_before":SLOW5_DOUBLE,
"read_number": SLOW5_INT32_T,
"start_mux": SLOW5_UINT8_T,
"start_time": SLOW5_UINT64_T,
"end_reason": None}
for a in user_aux_types:
if user_aux_types[a] is None:
continue
if a not in py_aux_types:
self.logger.error("_aux_type_validation {}: {} user aux field not in pyslow5 aux_types".format(a, user_aux_types[a]))
return None
if user_aux_types[a] == py_aux_types[a]:
slow5_aux_types[a] = C_aux_types[a]
else:
self.logger.error("_aux_type_validation {}: {} user aux field type mismatch with pyslow5 aux_types".format(a, user_aux_types[a]))
return None
return slow5_aux_types
def _record_type_validation(self, user_record, aux=None):
'''
internal function to validate and convert aux types before pushing to C side
returns None, None on error
'''
py_record_types = {"read_id": type("string"),
"read_group": type(1),
"digitisation": type(1.0),
"offset": type(1.0),
"range": type(1.0),
"sampling_rate": type(1.0),
"len_raw_signal": type(10),
"signal": type(np.array([1, 2, 3], np.int16))}
py_aux_types = {"channel_number": type("string"),
"median_before": type(1.0),
"read_number": type(10),
"start_mux": type(1),
"start_time": type(100),
"end_reason": None}
new_aux = {}
for a in user_record:
if user_record[a] is None:
continue
if a not in py_record_types:
self.logger.error("_record_type_validation {}: {} user primary field not in pyslow5 record_types".format(a, user_record[a]))
return None, None
if type(user_record[a]) != py_record_types[a]:
self.logger.error("_record_type_validation {}: {} user primary field type mismatch with pyslow5 record_types".format(a, user_record[a]))
return None, None
# check aux if given
if aux is not None:
self.logger.debug("_record_type_validation: doing aux stuff...")
for a in aux:
if a not in py_aux_types:
self.logger.error("_record_type_validation {}: {} user aux field not in pyslow5 aux_types".format(a, aux[a]))
return None, None
if aux[a] is None:
continue
if type(aux[a]) != py_aux_types[a]:
self.logger.error("_record_type_validation {}: {} user aux field type mismatch with pyslow5 aux_types".format(a, aux[a]))
return None, None
else:
self.logger.debug("_record_type_validation: aux passed tests...")
if a == "channel_number":
self.channel_number_val=strdup(aux[a].encode())
new_aux[a] = aux[a]
elif a == "median_before":
self.median_before_val = <double>aux[a]
new_aux[a] = aux[a]
elif a == "read_number":
self.read_number_val = <int32_t>aux[a]
new_aux[a] = aux[a]
elif a == "start_mux":
self.start_mux_val = <uint8_t>aux[a]
new_aux[a] = aux[a]
elif a == "start_time":
self.start_time_val = <uint64_t>aux[a]
new_aux[a] = aux[a]
elif a == "end_reason":
continue
self.logger.debug("_record_type_validation: doing aux stuff...")
return user_record, new_aux
def _multi_record_type_validation(self, user_record, aux=None):
'''
internal function to validate and convert aux types before pushing to C side
returns None, None on error
'''
py_record_types = {"read_id": type("string"),
"read_group": type(1),
"digitisation": type(1.0),
"offset": type(1.0),
"range": type(1.0),
"sampling_rate": type(1.0),
"len_raw_signal": type(10),
"signal": type(np.array([1, 2, 3], np.int16))}
py_aux_types = {"channel_number": type("string"),
"median_before": type(1.0),
"read_number": type(10),
"start_mux": type(1),
"start_time": type(100),
"end_reason": None}
new_aux = {}
for a in user_record:
if user_record[a] is None:
continue
if a not in py_record_types:
self.logger.error("_record_type_validation {}: {} user primary field not in pyslow5 record_types".format(a, user_record[a]))
return None, None
if type(user_record[a]) != py_record_types[a]:
self.logger.error("_record_type_validation {}: {} user primary field type mismatch with pyslow5 record_types".format(a, user_record[a]))
return None, None
# check aux if given
if aux is not None:
self.logger.debug("_record_type_validation: doing aux stuff...")
for a in aux:
if a not in py_aux_types:
self.logger.error("_record_type_validation {}: {} user aux field not in pyslow5 aux_types".format(a, aux[a]))
return None, None
if aux[a] is None:
continue
if type(aux[a]) != py_aux_types[a]:
self.logger.error("_record_type_validation {}: {} user aux field type mismatch with pyslow5 aux_types".format(a, aux[a]))
return None, None
else:
self.logger.debug("_record_type_validation: aux passed tests...")
if a == "channel_number":
new_aux[a] = aux[a]
elif a == "median_before":
new_aux[a] = aux[a]
elif a == "read_number":
new_aux[a] = aux[a]
elif a == "start_mux":
new_aux[a] = aux[a]
elif a == "start_time":
new_aux[a] = aux[a]
elif a == "end_reason":
continue
self.logger.debug("_record_type_validation: aux stuff done")
return user_record, new_aux
def write_header(self, header, read_group=0):
'''
write slow5 header to file.
takes header dic for attributes, then write once.
Must write readgroup 0 before 1, 1 before 2, etc
'''
checked_header = self._header_type_validation(header)
errors = False
if not self.header_add_attr_state:
if read_group > 0:
self.logger.error("write_header: You must set read_group=0 first")
self.logger.error("write_header: headers failed to initialise.")
return -1
for h in checked_header:
ret = slow5_hdr_add_attr(h.encode(), self.s5.header)
if ret < 0:
self.logger.error("write_header: slow5_hdr_add_attr {}: {} could not initialise to C s5.header struct".format(h, checked_header[h]))
errors = True
else:
self.header_add_attr_state = True
if read_group > 0 and self.header_add_attr_state:
ret = slow5_hdr_add_rg(self.s5.header)
if ret < 0:
self.logger.error("write_header: slow5_hdr_add_rg failed for read_group: {}".format(read_group))
errors = True
if errors:
self.logger.error("write_header: headers failed to initialise.")
return -1
for h in checked_header:
ret = slow5_hdr_set(h.encode(), checked_header[h].encode(), read_group, self.s5.header)
if ret < 0:
self.logger.error("write_header: slow5_hdr_set {}: {} could not set to C s5.header struct".format(h, checked_header[h]))
errors = True
if not errors:
return 0
else:
self.logger.error("write_header: errors encountered setting up header, aborting write")
# sys.exit(1)
return -1
def write_record(self, record, aux=None):
'''
write a single record
check self.header_state, if False, header needs to be written. Use aux types to do first check.
if the validation works, then write the header just before the first record is written.
This should make the user experience a lot less complicated and have less steps
'''
aux_types = {"channel_number": type("string"),
"median_before": type(1.0),
"read_number": type(10),
"start_mux": type(1),
"start_time": type(100),
"end_reason": None}
self.logger.debug("write_record: _record_type_validation running")
checked_record, checked_aux = self._record_type_validation(record, aux)
self.logger.debug("write_record: _record_type_validation done")
# check if in append state
# if so, we can skip header setup
if self.state == 2:
self.header_state = True
# if all checks are good, test self.header_state for 1 time write
if not self.header_state:
self.logger.debug("write_record: checking header stuff...")
error = False
if aux is not None:
if checked_aux is not None:
slow5_aux_types = self._aux_header_type_validation(aux_types)
for a in slow5_aux_types:
if slow5_aux_types[a] is None:
continue
ret = slow5_aux_add(a.encode(), slow5_aux_types[a], self.s5.header)
if ret < 0:
self.logger.error("write_record: slow5_aux_add {}: {} could not set to C s5.header.aux_meta struct".format(a, checked_aux[a]))
error = True
else:
error = True
if error:
self.logger.error("write_record: aux_meta fields failed to initialise")
return -1
# write the header
self.logger.debug("write_record: writting header...")
ret = slow5_hdr_write(self.s5)
if ret < 0:
self.logger.error("write_record: slow5_hdr_write could not write header")
return -1
# set state true so only done once
self.header_state = True
self.logger.debug("write_record: header written")
# Add values to read struct
self.logger.debug("write_record: slow5_rec_init()")
self.write = slow5_rec_init()
if self.write == NULL:
self.logger.error("write_record: failed to allocate space for slow5 record (self.write)")
return -1
self.logger.debug("write_record: self.write assignments...")
checked_record["read_id"] = checked_record["read_id"].encode()
self.write.read_id = strdup(checked_record["read_id"])
self.write.read_id_len = len(checked_record["read_id"])
self.write.read_group = checked_record["read_group"]
self.write.digitisation = checked_record["digitisation"]
self.write.offset = checked_record["offset"]
self.write.range = checked_record["range"]
self.write.sampling_rate = checked_record["sampling_rate"]
self.write.len_raw_signal = checked_record["len_raw_signal"]
self.logger.debug("write_record: self.write.raw_signal malloc...")
self.write.raw_signal = <int16_t *> malloc(sizeof(int16_t)*checked_record["len_raw_signal"])
self.logger.debug("write_record: self.write.raw_signal malloc done")
self.logger.debug("write_record: self.write assignments done")
self.logger.debug("write_record: self.write processing raw_signal")
start_write_copy_signal = time.time()
# grabs buffer of numby array so the for loop operats in C not python = super fast
memview = memoryview(checked_record["signal"])
for i in range(checked_record["len_raw_signal"]):
self.write.raw_signal[i] = memview[i]
# for i in range(checked_record["len_raw_signal"]):
# self.write.raw_signal[i] = checked_record["signal"][i]
end_write_copy_signal = (time.time() - start_write_copy_signal)
self.total_single_write_time = self.total_single_write_time + end_write_copy_signal
self.logger.debug("write_record: self.write raw_signal done")
if aux:
self.logger.debug("write_record: aux stuff...")
if checked_aux is None:
self.logger.error("write_record: checked_aux is None".format(a, checked_aux[a]))
return -1
for a in checked_aux:
self.logger.debug("write_record: checked_aux: {}: {}".format(a, checked_aux[a]))
if checked_aux[a] is None:
continue
if a == "channel_number":
self.logger.debug("write_record: slow5_aux_set_string running...")
self.logger.debug("write_record: slow5_aux_set_string type: {}".format(type(checked_aux[a])))
ret = slow5_aux_set_string(self.write, self.channel_number, <const char *>self.channel_number_val, self.s5.header)
self.logger.debug("write_record: slow5_aux_set_string running done: ret = {}".format(ret))
if ret < 0:
self.logger.error("write_record: slow5_aux_set_string could not write aux value {}: {}".format(a, checked_aux[a]))
#### We should free here
return -1
elif a == "median_before":
ret = slow5_aux_set(self.write, self.median_before, <const void *>&self.median_before_val, self.s5.header)
elif a == "read_number":
ret = slow5_aux_set(self.write, self.read_number, <const void *>&self.read_number_val, self.s5.header)
elif a == "start_mux":
ret = slow5_aux_set(self.write, self.start_mux, <const void *>&self.start_mux_val, self.s5.header)
elif a == "start_time":
ret = slow5_aux_set(self.write, self.start_time, <const void *>&self.start_time_val, self.s5.header)
elif a == "end_reason":
# not implemented yet becuase of variability in ONT versioning
ret = 0
if ret < 0:
self.logger.error("write_record: slow5_aux_set could not write aux value {}: {}".format(a, checked_aux[a]))
return -1
self.logger.debug("write_record: aux stuff done")
self.logger.debug("write_record: slow5_write()")
# write the record
ret = slow5_write(self.write, self.s5)
self.logger.debug("write_record: slow5_write() ret: {}".format(ret))
if aux is not None:
free(self.channel_number_val)
self.channel_number_val = NULL
self.median_before_val = -1.0
self.read_number_val = -1
self.start_mux_val = -1
self.start_time_val = -1
# free memory
self.logger.debug("write_record: slow5_rec_free()")
slow5_rec_free(self.write)
self.write = NULL
self.logger.debug("write_record: function complete, returning 0")
return 0
def write_record_batch(self, records, threads=4, batchsize=4096, aux=None):
'''
write a batch of records
same as write_record, but in batches
records = dic of read rics, where the key for each is the readID
if aux, aux is also a dic of dics, whhere the key for each is teh readID
records = {readID_0: {read_dic}, readID_1: {read_dic}}
'''
start_multi_write = time.time()
aux_types = {"channel_number": type("string"),
"median_before": type(1.0),
"read_number": type(10),
"start_mux": type(1),
"start_time": type(100),
"end_reason": None}
# check an empty dic wasn't given
if aux is not None:
if len(aux) == 0:
aux = None
self.logger.debug("write_record_batch: Setting up batching...")
num_reads = len(records)
read_list = list(records.keys())
if num_reads > batchsize:
batches = self._get_batches(read_list, size=batchsize)
else:
batches = self._get_batches(read_list, size=num_reads)
self.logger.debug("write_record_batch: batch for loop start")
for batch in chain(batches):
batch_len = len(batch)
self.twrite = <slow5_rec_t **> malloc(sizeof(slow5_rec_t*)*batch_len)
self.logger.debug("write_record_batch: _record_type_validation running")
checked_records = {}
checked_auxs = {}
self.channel_number_val_array = <char **> malloc(sizeof(char*)*batch_len)
self.median_before_val_array = <double *> malloc(sizeof(double)*batch_len)
self.read_number_val_array = <int32_t *> malloc(sizeof(int32_t)*batch_len)
self.start_mux_val_array = <uint8_t *> malloc(sizeof(uint8_t)*batch_len)
self.start_time_val_array = <uint64_t *> malloc(sizeof(uint64_t)*batch_len)
for i, idx in enumerate(batch):
if aux is not None:
checked_record, checked_aux = self._multi_record_type_validation(records[idx], aux[idx])
checked_records[idx] = checked_record
for a in checked_aux:
if a == "channel_number":
self.channel_number_val_array[i] = strdup(checked_aux[a].encode())
elif a == "median_before":
self.median_before_val_array[i] = <double>checked_aux[a]
elif a == "read_number":
self.read_number_val_array[i] = <int32_t>checked_aux[a]
elif a == "start_mux":
self.start_mux_val_array[i] = <uint8_t>checked_aux[a]
elif a == "start_time":
self.start_time_val_array[i] = <uint64_t>checked_aux[a]
checked_auxs[idx] = checked_aux
else:
checked_record, checked_aux = self._record_type_validation(records[idx], aux)
checked_records[idx] = checked_record
self.logger.debug("write_record_batch: _record_type_validation done")
if len(checked_aux) == 0:
checked_aux = None
for idx in range(batch_len):
# check if in append state
# if so, we can skip header setup
if self.state == 2:
self.header_state = True
# if all checks are good, test self.header_state for 1 time write
if not self.header_state:
self.logger.debug("write_record_batch: checking header stuff...")
error = False
if aux is not None:
if checked_aux is not None:
slow5_aux_types = self._aux_header_type_validation(aux_types)
for a in slow5_aux_types:
if slow5_aux_types[a] is None:
continue
ret = slow5_aux_add(a.encode(), slow5_aux_types[a], self.s5.header)
if ret < 0:
self.logger.error("write_record_batch: slow5_aux_add {}: {} could not set to C s5.header.aux_meta struct".format(a, checked_aux[a]))
error = True
else:
error = True
if error:
self.logger.error("write_record_batch: aux_meta fields failed to initialise")
return -1
# write the header
self.logger.debug("write_record_batch: writting header...")
ret = slow5_hdr_write(self.s5)
if ret < 0:
self.logger.error("write_record_batch: slow5_hdr_write could not write header")
return -1
# set state true so only done once
self.header_state = True
self.logger.debug("write_record_batch: header written")
# Add values to read struct
self.logger.debug("write_record_batch: slow5_rec_init()")
self.twrite[idx] = slow5_rec_init()
if self.twrite[idx] == NULL:
self.logger.error("write_record_batch: failed to allocate space for slow5 record (self.twrite[idx])")
return -1
self.logger.debug("write_record_batch: self.write assignments...")
checked_records[batch[idx]]["read_id"] = checked_records[batch[idx]]["read_id"].encode()
self.twrite[idx].read_id = strdup(checked_records[batch[idx]]["read_id"])
self.twrite[idx].read_id_len = len(checked_records[batch[idx]]["read_id"])
self.twrite[idx].read_group = checked_records[batch[idx]]["read_group"]
self.twrite[idx].digitisation = checked_records[batch[idx]]["digitisation"]
self.twrite[idx].offset = checked_records[batch[idx]]["offset"]
self.twrite[idx].range = checked_records[batch[idx]]["range"]
self.twrite[idx].sampling_rate = checked_records[batch[idx]]["sampling_rate"]
self.twrite[idx].len_raw_signal = checked_records[batch[idx]]["len_raw_signal"]
self.logger.debug("write_record_batch: self.write.raw_signal malloc...")
self.twrite[idx].raw_signal = <int16_t *> malloc(sizeof(int16_t)*checked_records[batch[idx]]["len_raw_signal"])
self.logger.debug("write_record_batch: self.write.raw_signal malloc done")
self.logger.debug("write_record_batch: self.write assignments done")
self.logger.debug("write_record_batch: self.write processing raw_signal")
start_write_copy_signal = time.time()
# grabs buffer of numby array so the for loop operats in C not python = super fast
memview = memoryview(checked_records[batch[idx]]["signal"])
for i in range(checked_records[batch[idx]]["len_raw_signal"]):
self.twrite[idx].raw_signal[i] = memview[i]
# for i in range(checked_records[batch[idx]]["len_raw_signal"]):
# self.twrite[idx].raw_signal[i] = checked_records[batch[idx]]["signal"][i]
end_write_copy_signal = (time.time() - start_write_copy_signal)
self.total_multi_write_signal_time = self.total_multi_write_signal_time + end_write_copy_signal
self.logger.debug("write_record_batch: self.write raw_signal done")
if aux is not None:
self.logger.debug("write_record_batch: aux stuff...")
if checked_auxs[batch[idx]] is None:
self.logger.error("write_record_batch: checked_aux is None".format(a, checked_auxs[batch[idx]][a]))
return -1
for a in checked_auxs[batch[idx]]:
self.logger.debug("write_record_batch: checked_aux: {}: {}".format(a, checked_auxs[batch[idx]][a]))
if checked_auxs[batch[idx]][a] is None:
continue
if a == "channel_number":
self.logger.debug("write_record_batch: slow5_aux_set_string running...")
self.logger.debug("write_record_batch: slow5_aux_set_string type: {}".format(type(checked_auxs[batch[idx]][a])))
ret = slow5_aux_set_string(self.twrite[idx], self.channel_number, <const char *>self.channel_number_val_array[idx], self.s5.header)
self.logger.debug("write_record_batch: slow5_aux_set_string running done: ret = {}".format(ret))
if ret < 0:
self.logger.error("write_record_batch: slow5_aux_set_string could not write aux value {}: {}".format(a, checked_auxs[batch[idx]][a]))
#### We should free here
return -1
elif a == "median_before":
ret = slow5_aux_set(self.twrite[idx], self.median_before, <const void *>&self.median_before_val_array[idx], self.s5.header)
elif a == "read_number":
ret = slow5_aux_set(self.twrite[idx], self.read_number, <const void *>&self.read_number_val_array[idx], self.s5.header)
elif a == "start_mux":
ret = slow5_aux_set(self.twrite[idx], self.start_mux, <const void *>&self.start_mux_val_array[idx], self.s5.header)
elif a == "start_time":
ret = slow5_aux_set(self.twrite[idx], self.start_time, <const void *>&self.start_time_val_array[idx], self.s5.header)
elif a == "end_reason":
# not implemented yet becuase of variability in ONT versioning
ret = 0
if ret < 0:
self.logger.error("write_record_batch: slow5_aux_set could not write aux value {}: {}".format(a, checked_aux[a]))
return -1
self.logger.debug("write_record_batch: aux stuff done")
self.logger.debug("write_record_batch: slow5_write_batch()")
# write the record
if batch_len <= 0:
self.logger.debug("write_record_batch: batch_len 0 or less")
break
ret = slow5_write_batch(self.twrite, self.s5, batch_len, threads)
if ret < batch_len:
self.logger.error("write_record_batch: write failed")
return -1
self.logger.debug("write_record_batch: free()")
for i in range(batch_len):
slow5_rec_free(self.twrite[i])
free(self.twrite)
self.logger.debug("write_record_batch: free() aux")
if aux is not None:
for i in range(batch_len):
free(self.channel_number_val_array[i])
free(self.channel_number_val_array)
free(self.median_before_val_array)
free(self.read_number_val_array)
free(self.start_mux_val_array)
free(self.start_time_val_array)
end_multi_write = time.time() - start_multi_write
self.total_multi_write_time = self.total_multi_write_time + end_multi_write
# free memory
# self.twrite = NULL
self.logger.debug("write_record_batch: function complete, returning 0")
return 0
def close(self):
'''
close file so EOF is written
'''
if self.state in [1,2]:
if not self.close_state:
if self.s5 is not NULL:
slow5_close(self.s5)
self.close_state = True
self.logger.debug("{} closed".format(self.path))
else:
self.logger.warning("{} already closed".format(self.path))
elif self.state == 0:
if not self.close_state:
if self.s5 is not NULL:
slow5_close(self.s5)
self.close_state = True
self.logger.debug("{} closed".format(self.path))
else:
self.logger.warning("{} already closed".format(self.path))
else:
self.logger.error("{} not open for writing, remake class object to refresh".format(self.path))
return
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