def get_handler(config, databases):
'''Build the TaskHandler for the annotation pipelines. The
handler will not have registered tasks when returned.
Args:
config (dict): Config dictionary, which contains the command
line arguments and the entries from the config file.
databases (dict): The dictionary of files from a database
TaskHandler.
Returns:
handler.TaskHandler: A constructed TaskHandler.
'''
logger = logging.getLogger('AnnotateHandler')
if config['output_dir'] is None:
out_dir = path.basename(config['transcriptome'] + '.dammit')
else:
out_dir = config['output_dir']
directory = path.abspath(out_dir)
handler = TaskHandler(directory,
logger,
db='annotate',
backend=config['doit_backend'],
verbosity=config['verbosity'],
profile=config['profile'])
log.start_logging(path.join(directory, 'dammit.log'))
txome_fn = path.join(directory, path.basename(config['transcriptome']))
if not config['no_rename']:
name_map_fn = txome_fn + '.dammit.namemap.csv'
handler.register_task('rename-transcriptome',
get_rename_transcriptome_task(
path.abspath(config['transcriptome']),
txome_fn, name_map_fn, config['name']),
files={
'transcriptome': txome_fn,
'name_map': name_map_fn
})
else:
handler.register_task('copy-transcriptome',
get_copy_file_task(
path.abspath(config['transcriptome']),
txome_fn),
files={'transcriptome': txome_fn})
return handler
def handle_databases(self):
log.start_logging()
print(ui.header('submodule: databases', level=2))
handler = databases.get_handler(self.config_d)
if self.args.quick:
databases.build_quick_pipeline(handler, self.config_d,
self.databases_d)
else:
databases.build_default_pipeline(handler,
self.config_d,
self.databases_d,
with_uniref=self.args.full,
with_nr=self.args.nr)
if self.args.install:
return databases.install(handler)
else:
databases.check_or_fail(handler)
def handle_annotate(self):
log.start_logging()
print(ui.header('submodule: annotate', level=2))
db_handler = databases.get_handler(self.config_d)
if self.args.quick:
databases.build_quick_pipeline(db_handler, self.config_d,
self.databases_d)
else:
databases.build_default_pipeline(db_handler,
self.config_d,
self.databases_d,
with_uniref=self.args.full,
with_nr=self.args.nr)
if self.config_d['force'] is True:
utd_msg = '*All database tasks up-to-date.*'
ood_msg = '*Some database tasks out-of-date; '\
'FORCE is True, ignoring!'
uptodate, statuses = db_handler.print_statuses(
uptodate_msg=utd_msg, outofdate_msg=ood_msg)
else:
databases.check_or_fail(db_handler)
annotate_handler = annotate.get_handler(self.config_d,
db_handler.files)
if self.args.quick:
build_quick_pipeline(annotate_handler, self.config_d,
db_handler.files)
elif self.args.full:
build_full_pipeline(annotate_handler, self.config_d,
db_handler.files)
elif self.args.nr:
build_nr_pipeline(annotate_handler, self.config_d,
db_handler.files)
else:
build_default_pipeline(annotate_handler, self.config_d,
db_handler.files)
return annotate.run_annotation(annotate_handler)
import traceback
import shutil
import stat
import sys
import warnings as _warnings
from pkg_resources import Requirement, resource_filename, ResolutionError
from tempfile import mkdtemp
from doit.cmd_base import TaskLoader
from doit.doit_cmd import DoitMain
from doit.dependency import Dependency, DbmDB
from pytest import fixture
from dammit import log
log.start_logging(test=True)
logger = logging.getLogger('Tests')
'''
BATCH EFFECTS -- The Notorious A.T.G.
-------------------------------------
Shit your 'scripts ain't differential -
they're preferential
(-ly selected!)
from you read seq
to your DEseq
your biases are your analyses fallacies
your matrices
are make-believe
your shallow e-values swallowing your logic and your counts bouncin' --
you got BATCH EFFECTS
