def split_fasta_file(input_file_path,
dest_dir,
prefix='part',
number_of_sequences_per_file=20000):
debug('%s; src: %s, dest dir: %s' % (my_name(), input_file_path, dest_dir))
input = SequenceSource(input_file_path)
parts = []
next_part = 1
part_obj = None
while input.next():
if (input.pos - 1) % number_of_sequences_per_file == 0:
sys.stderr.write('\rCreating part: ~ %s' % (pp(next_part)))
sys.stderr.flush()
if part_obj:
part_obj.close()
file_path = os.path.join(dest_dir, prefix + '-%08d' % next_part)
parts.append(file_path)
next_part += 1
part_obj = open(file_path, 'w')
part_obj.write('>%s\n' % input.id)
part_obj.write('%s\n' % input.seq)
if part_obj:
part_obj.close()
sys.stderr.write('\n')
return parts
def copy_file(source_file, dest_file):
debug('%s; dest: "%s", src: "%s"' % (my_name(), source_file, dest_file))
try:
return shutil.copyfile(source_file, dest_file)
except IOError, e:
raise UtilsError, "copy failed due to the following reason: '%s' (src: %s, dst: %s)" \
% (e, source_file, dest_file)
def store_ids_from_b6_output(source_b6_output, dest_file):
debug('%s; dest: %s' % (my_name(), dest_file))
try:
b6 = B6Source(source_b6_output)
except IOError, e:
raise UtilsError, "open failed due to the following reason: '%s' (src: %s)" \
% (e, source_b6_output)
def store_ids_from_b6_output(source_b6_output, dest_file):
debug('%s; dest: %s' % (my_name(), dest_file))
try:
b6 = B6Source(source_b6_output)
except IOError, e:
raise UtilsError, "open failed due to the following reason: '%s' (src: %s)" \
% (e, source_b6_output)
def run_command(cmdline):
debug('%s; cmd: %s' % (my_name(), cmdline))
try:
if subprocess.call(cmdline, shell = True) < 0:
raise UtilsError, "command was terminated by signal: %d" % (-retcode)
except OSError, e:
raise UtilsError, "command was failed for the following reason: '%s' ('%s')" % (e, cmdline)
def split_fasta_file(input_file_path, dest_dir, prefix = 'part', number_of_sequences_per_file = 20000):
debug('%s; src: %s, dest dir: %s' % (my_name(), input_file_path, dest_dir))
input = SequenceSource(input_file_path)
parts = []
next_part = 1
part_obj = None
while input.next():
if (input.pos - 1) % number_of_sequences_per_file == 0:
sys.stderr.write('\rCreating part: ~ %s' % (pp(next_part)))
sys.stderr.flush()
if part_obj:
part_obj.close()
file_path = os.path.join(dest_dir, prefix + '-%08d' % next_part)
parts.append(file_path)
next_part += 1
part_obj = open(file_path, 'w')
part_obj.write('>%s\n' % input.id)
part_obj.write('%s\n' % input.seq)
if part_obj:
part_obj.close()
sys.stderr.write('\n')
return parts
def copy_file(source_file, dest_file):
debug('%s; dest: "%s", src: "%s"' % (my_name(), source_file, dest_file))
try:
return shutil.copyfile(source_file, dest_file)
except IOError, e:
raise UtilsError, "copy failed due to the following reason: '%s' (src: %s, dst: %s)" \
% (e, source_file, dest_file)
def init_modules(self):
mod_base = self.constants.dirs['modules']
for file in os.listdir(mod_base):
if file.startswith('mod_') and file.endswith('.py'):
mod_name = file[4:-3]
self.modules[mod_name] = imp.load_source(mod_name, os.path.join(mod_base, file))
debug('module "%s" found' % mod_name)
def concatenate_files(dest_file, file_list):
debug('%s; dest: "%s"' % (my_name(), dest_file))
dest_file_obj = open(dest_file, 'w')
for chunk_path in file_list:
for line in open(chunk_path):
dest_file_obj.write(line)
return dest_file_obj.close()
def refine_b6(source_file, dest_file, params):
# FIXME: check if source_file is a valid m8 output.
debug('%s; dest: %s' % (my_name(), dest_file))
try:
b6 = B6Source(source_file)
except IOError, e:
raise UtilsError, "open failed due to the following reason: '%s' (src: %s)" \
% (e, source_file)
def concatenate_files(dest_file, file_list):
debug('%s; dest: "%s"' % (my_name(), dest_file))
dest_file_obj = open(dest_file, 'w')
for chunk_path in file_list:
for line in open(chunk_path):
dest_file_obj.write(line)
return dest_file_obj.close()
def init_modules(self):
mod_base = self.constants.dirs['modules']
for file in os.listdir(mod_base):
if file.startswith('mod_') and file.endswith('.py'):
mod_name = file[4:-3]
self.modules[mod_name] = imp.load_source(
mod_name, os.path.join(mod_base, file))
debug('module "%s" found' % mod_name)
def refine_b6(source_file, dest_file, params):
# FIXME: check if source_file is a valid m8 output.
debug('%s; dest: %s' % (my_name(), dest_file))
try:
b6 = B6Source(source_file)
except IOError, e:
raise UtilsError, "open failed due to the following reason: '%s' (src: %s)" \
% (e, source_file)
def split_file(ids_file,
source_file,
filtered_dest_file,
survived_dest_file,
type='fasta'):
"""splits reads in input file into two files based on ids_file
for read_id in input:
if read_id in list_of_ids:
--> filtered_dest_file
else:
--> survived dest_file
"""
debug('%s; src: "%s" (%s), filtered_dest: "%s", survived_dest: "%s"'\
% (my_name(), source_file, type, filtered_dest_file, survived_dest_file))
try:
ids_to_filter = set([id.strip() for id in open(ids_file).readlines()])
except IOError:
raise FilterError, 'Hit IDs file missing ("%s").' \
% (ids_to_filter)
if type == 'fasta':
STORE = lambda e, f: f.write('>%s\n%s\n' % (e.id, e.seq))
input = SequenceSource(source_file)
filtered_output = open(filtered_dest_file, 'w')
survived_output = open(survived_dest_file, 'w')
filtered_count, survived_count = 0, 0
while input.next():
if input.pos % 10000 == 0 or input.pos == 1:
sys.stderr.write('\rSplitting FASTA file: ~ %s' %
(pp(input.pos)))
sys.stderr.flush()
if input.id in ids_to_filter:
ids_to_filter.remove(input.id)
STORE(input, filtered_output)
filtered_count += 1
else:
STORE(input, survived_output)
survived_count += 1
sys.stderr.write('\n')
filtered_output.close()
survived_output.close()
debug('%s; done. of %s total reads, filtered: %s, survived: %s.'\
% (my_name(), pp(filtered_count + survived_count),\
pp(filtered_count), pp(survived_count)))
else:
raise UtilsError, "type '%s' is not implemented" % (type)
return True
def run_command(cmdline):
debug('%s; cmd: %s' % (my_name(), cmdline))
try:
if subprocess.call(cmdline, shell=True) < 0:
raise UtilsError, "command was terminated by signal: %d" % (
-retcode)
except OSError, e:
raise UtilsError, "command was failed for the following reason: '%s' ('%s')" % (
e, cmdline)
def search(m):
parts = m.files['parts']
for part in parts:
params = {'input': part, 'output': part + '.b6', 'target': m.target_db,
'log': part + '.log', 'cmdparams': ' '.join(m.cmdparams)}
debug('searching part %d/%d (log: %s)' % (parts.index(part) + 1, len(parts), params['log']))
cmdline = SEARCH_COMMAND % params
utils.run_command(cmdline)
dest_file = m.files['search_output']
utils.concatenate_files(dest_file, [part + '.b6' for part in m.files['parts']])
def split_file(ids_file, source_file, filtered_dest_file, survived_dest_file, type = 'fasta'):
"""splits reads in input file into two files based on ids_file
for read_id in input:
if read_id in list_of_ids:
--> filtered_dest_file
else:
--> survived dest_file
"""
debug('%s; src: "%s" (%s), filtered_dest: "%s", survived_dest: "%s"'\
% (my_name(), source_file, type, filtered_dest_file, survived_dest_file))
try:
ids_to_filter = set([id.strip() for id in open(ids_file).readlines()])
except IOError:
raise FilterError, 'Hit IDs file missing ("%s").' \
% (ids_to_filter)
if type == 'fasta':
STORE = lambda e, f: f.write('>%s\n%s\n' % (e.id, e.seq))
input = SequenceSource(source_file)
filtered_output = open(filtered_dest_file, 'w')
survived_output = open(survived_dest_file, 'w')
filtered_count, survived_count = 0, 0
while input.next():
if input.pos % 10000 == 0 or input.pos == 1:
sys.stderr.write('\rSplitting FASTA file: ~ %s' % (pp(input.pos)))
sys.stderr.flush()
if input.id in ids_to_filter:
ids_to_filter.remove(input.id)
STORE(input, filtered_output)
filtered_count += 1
else:
STORE(input, survived_output)
survived_count += 1
sys.stderr.write('\n')
filtered_output.close()
survived_output.close()
debug('%s; done. of %s total reads, filtered: %s, survived: %s.'\
% (my_name(), pp(filtered_count + survived_count),\
pp(filtered_count), pp(survived_count)))
else:
raise UtilsError, "type '%s' is not implemented" % (type)
return True
def search(m):
parts = m.files["parts"]
for part in parts:
params = {
"input": part,
"output": part + ".b6",
"target": m.target_db,
"log": part + ".log",
"cmdparams": " ".join(m.cmdparams),
}
debug("searching part %d/%d (log: %s)" % (parts.index(part) + 1, len(parts), params["log"]))
cmdline = SEARCH_COMMAND % params
utils.run_command(cmdline)
dest_file = m.files["search_output"]
utils.concatenate_files(dest_file, [part + ".b6" for part in m.files["parts"]])
def __init__(self, args, constants):
if args:
self.args = args
self.constants = constants
self.base_work_dir = self.args.base_work_dir.replace(' ', '_')
self.dataset_name = self.args.dataset_name.replace(' ', '_')
self.input = self.args.input
self.dataset_root_dir = os.path.join(self.base_work_dir, self.dataset_name)
self.filters = []
self.modules = {}
debug('Initializing configuration')
self.init_modules()
self.init_essential_files_and_directories()
self.init_filters_config(args.filters_config)
self.init_chain_of_filters()
debug('Config class is initialized with %d modules and %d filters'\
% (len(self.modules), len(self.filters)))
def __init__(self, args, constants):
if args:
self.args = args
self.constants = constants
self.base_work_dir = self.args.base_work_dir.replace(' ', '_')
self.dataset_name = self.args.dataset_name.replace(' ', '_')
self.input = self.args.input
self.dataset_root_dir = os.path.join(self.base_work_dir,
self.dataset_name)
self.filters = []
self.modules = {}
debug('Initializing configuration')
self.init_modules()
self.init_essential_files_and_directories()
self.init_filters_config(args.filters_config)
self.init_chain_of_filters()
debug('Config class is initialized with %d modules and %d filters'\
% (len(self.modules), len(self.filters)))
def delete_files_in_dir(dir):
debug('%s; removing content of "%s"' % (my_name(), dir))
for f in os.listdir(dir):
os.unlink(os.path.join(dir, f))
def init_filters_config(self, config_file_path):
filters_config = ConfigParserWrapper(config_file_path)
filters_config.read(config_file_path)
for section in filters_config.sections():
filter = Filter(section)
filter.name = filters_config.get(section,
'filter_name').replace(' ', '_')
# check if the target database, which happens to be the section name,
# exists
if not (os.path.exists(section) and os.access(section, os.R_OK)):
raise ConfigError, 'Bad target (file not found / no read permission): "%s"' % section
# assign module
module_from_config = filters_config.get(section, 'module')
if not self.modules.has_key(module_from_config):
raise ConfigError, 'Unknown module for filter "%s": "%s".\nAvailable modules:\n%s' \
% (filter.name, module_from_config, ', '.join(self.modules.keys()))
else:
filter.module = self.modules[module_from_config]
# check the availability of the functions and the execution order, if the default
# behavior has been changed manually in the config file
if filters_config.has_option(section, 'execute'):
execute_list_from_config = [
e.strip()
for e in filters_config.get(section, 'execute').split(',')
]
for item in execute_list_from_config:
if item not in filter.module.FUNCTIONS_ORDER:
raise ConfigError, 'Unknown function for module "%s" in "%s": "%s".\nAvailable functions: %s' \
% (module_from_config, filter.name, item, ', '.join(filter.module.FUNCTIONS_ORDER))
if len(execute_list_from_config) != len(
list(set(execute_list_from_config))):
raise ConfigError, 'Functions cannot be executed more than once: %s' \
% (', '.join(execute_list_from_config))
# make sure the order is right.
t = [
filter.module.FUNCTIONS_ORDER.index(i)
for i in execute_list_from_config
]
if False in [t[i] > t[i - 1] for i in range(1, len(t))]:
raise ConfigError, 'Order of functions to be executed is not correct: %s\nFunctions should follow this order: %s' \
% (', '.join(execute_list_from_config), ', '.join(filter.module.FUNCTIONS_ORDER))
filter.execution_order = execute_list_from_config
debug(
'filter module functions execution order has been set: "%s"'
% (filter.execution_order))
# store command line parameters from the config file
for option in [
o for o in filters_config.options(section)
if o.startswith('cmdparam.')
]:
param = '.'.join(option.split('.')[1:])
opt = filters_config.get(section, option)
filter.cmdparams.append('%s %s' % (param, opt))
debug('command line params for filter "%s": %s ' %
(filter.name, filter.cmdparams))
# store post-search refinement filters from the config file
for option in [
o for o in filters_config.options(section)
if o.startswith('rfnparam.')
]:
param = '.'.join(option.split('.')[1:])
opt = filters_config.get(section, option)
if param in filter.get_refinement_params():
filter.rfnparams[param] = filter.module.ALLOWED_RFNPARAMS[
param](opt)
else:
raise ConfigError, 'Unknown refinement parameter for filter "%s": "%s"' \
% (filter.name, param)
debug('refinement line params for filter "%s": %s ' %
(filter.name, filter.rfnparams))
# take care of file paths and directories
J = lambda x: os.path.join(filter.dirs['output'], x)
filter.dirs['output'] = os.path.join(self.dataset_root_dir,
filter.name)
filter.dirs['parts'] = J('parts')
filter.files['search_output'] = J('01_raw_hits.txt')
filter.files['refined_search_output'] = J('02_refined_hits.txt')
filter.files['hit_ids'] = J('03_hits.ids')
filter.files['filtered_reads'] = J('04_filtered.fa')
filter.files['survived_reads'] = J('05_survived.fa')
self.filters.append(filter)
def delete_files_in_dir(dir):
debug('%s; removing content of "%s"' % (my_name(), dir))
for f in os.listdir(dir):
os.unlink(os.path.join(dir, f))
def init_filters_config(self, config_file_path):
filters_config = ConfigParserWrapper(config_file_path)
filters_config.read(config_file_path)
for section in filters_config.sections():
filter = Filter(section)
filter.name = filters_config.get(section, 'filter_name').replace(' ', '_')
# check if the target database, which happens to be the section name,
# exists
if not (os.path.exists(section) and os.access(section, os.R_OK)):
raise ConfigError, 'Bad target (file not found / no read permission): "%s"' % section
# assign module
module_from_config = filters_config.get(section, 'module')
if not self.modules.has_key(module_from_config):
raise ConfigError, 'Unknown module for filter "%s": "%s".\nAvailable modules:\n%s' \
% (filter.name, module_from_config, ', '.join(self.modules.keys()))
else:
filter.module = self.modules[module_from_config]
# check the availability of the functions and the execution order, if the default
# behavior has been changed manually in the config file
if filters_config.has_option(section, 'execute'):
execute_list_from_config = [e.strip() for e in filters_config.get(section, 'execute').split(',')]
for item in execute_list_from_config:
if item not in filter.module.FUNCTIONS_ORDER:
raise ConfigError, 'Unknown function for module "%s" in "%s": "%s".\nAvailable functions: %s' \
% (module_from_config, filter.name, item, ', '.join(filter.module.FUNCTIONS_ORDER))
if len(execute_list_from_config) != len(list(set(execute_list_from_config))):
raise ConfigError, 'Functions cannot be executed more than once: %s' \
% (', '.join(execute_list_from_config))
# make sure the order is right.
t = [filter.module.FUNCTIONS_ORDER.index(i) for i in execute_list_from_config]
if False in [t[i] > t[i - 1] for i in range(1, len(t))]:
raise ConfigError, 'Order of functions to be executed is not correct: %s\nFunctions should follow this order: %s' \
% (', '.join(execute_list_from_config), ', '.join(filter.module.FUNCTIONS_ORDER))
filter.execution_order = execute_list_from_config
debug('filter module functions execution order has been set: "%s"' % (filter.execution_order))
# store command line parameters from the config file
for option in [o for o in filters_config.options(section) if o.startswith('cmdparam.')]:
param = '.'.join(option.split('.')[1:])
opt = filters_config.get(section, option)
filter.cmdparams.append('%s %s' % (param, opt))
debug('command line params for filter "%s": %s ' % (filter.name, filter.cmdparams))
# store post-search refinement filters from the config file
for option in [o for o in filters_config.options(section) if o.startswith('rfnparam.')]:
param = '.'.join(option.split('.')[1:])
opt = filters_config.get(section, option)
if param in filter.get_refinement_params():
filter.rfnparams[param] = filter.module.ALLOWED_RFNPARAMS[param](opt)
else:
raise ConfigError, 'Unknown refinement parameter for filter "%s": "%s"' \
% (filter.name, param)
debug('refinement line params for filter "%s": %s ' % (filter.name, filter.rfnparams))
# take care of file paths and directories
J = lambda x: os.path.join(filter.dirs['output'], x)
filter.dirs['output'] = os.path.join(self.dataset_root_dir, filter.name)
filter.dirs['parts'] = J('parts')
filter.files['search_output'] = J('01_raw_hits.txt')
filter.files['refined_search_output'] = J('02_refined_hits.txt')
filter.files['hit_ids'] = J('03_hits.ids')
filter.files['filtered_reads'] = J('04_filtered.fa')
filter.files['survived_reads'] = J('05_survived.fa')
self.filters.append(filter)