def gemini_case_obj(gemini_db_path):
"""Return a case object extracted from gemini database"""
_case = get_cases(gemini_db_path, variant_mode='gemini')[0]
yield _case
def gemini_sv_case_obj(gemini_sv_db_path):
"""Return a case object extracted from gemini database"""
_case = get_cases(gemini_sv_db_path, variant_mode='gemini')[0]
_case['variant_type'] = 'sv'
yield _case
def view(ctx, host, port, debug, pattern, family_file, family_type,
variant_source, root, no_browser, phenomizer):
"""Visualize DNA variant resources.
1. Look for variant source(s) to visualize and inst. the right plugin
"""
root = root or ctx.obj.get('root') or os.path.expanduser("~/.puzzle")
phenomizer_auth = phenomizer or ctx.obj.get('phenomizer_auth')
BaseConfig.PHENOMIZER_AUTH = True if ctx.obj.get('phenomizer_auth') else False
BaseConfig.STORE_ENABLED = True
if variant_source is None:
logger.info("Root directory is: {}".format(root))
db_path = os.path.join(root, 'puzzle_db.sqlite3')
logger.info("db path is: {}".format(db_path))
if not os.path.exists(db_path):
logger.warn("database not initialized, run 'puzzle init'")
ctx.abort()
if os.path.isfile(root):
logger.error("'root' can't be a file")
ctx.abort()
store = SqlStore(db_path, phenomizer_auth=phenomizer_auth)
for case_obj in store.cases():
if case_obj.variant_mode == 'gemini':
if not GEMINI:
logger.error("Need to have gemini instaled to view gemini database")
ctx.abort()
else:
logger.info("Using in memory database")
store = SqlStore('sqlite:///:memory:', phenomizer_auth=phenomizer_auth)
store.set_up()
cases = []
if os.path.isfile(variant_source):
file_type = get_file_type(variant_source)
#Test if gemini is installed
if file_type == 'unknown':
logger.error("File has to be vcf or gemini db")
ctx.abort()
elif file_type == 'gemini':
#Check if gemini is installed
if not GEMINI:
logger.error("Need to have gemini installed to use gemini plugin")
ctx.abort()
variant_type = get_variant_type(variant_source)
cases = get_cases(
variant_source=variant_source,
case_lines=family_file,
case_type=family_type,
variant_type=variant_type,
variant_mode=file_type
)
else:
for file in path(variant_source).walkfiles(pattern):
file_type = get_file_type(file)
if file_type != 'unknown':
variant_type = get_variant_type(file)
#Test if gemini is installed
if file_type == 'gemini':
if not GEMINI:
logger.error("Need to have gemini installed to use gemini plugin")
ctx.abort()
for case in get_cases(
variant_source=file,
case_type=family_type,
variant_type=variant_type,
variant_mode=file_type):
cases.append(case)
for case_obj in cases:
if store.case(case_obj.case_id) is not None:
logger.warn("{} already exists in the database"
.format(case_obj.case_id))
continue
# extract case information
logger.debug("adding case: {}".format(case_obj.case_id))
store.add_case(case_obj, vtype=case_obj.variant_type, mode=case_obj.variant_mode)
logger.debug("Plugin setup was succesfull")
BaseConfig.PUZZLE_BACKEND = store
BaseConfig.UPLOAD_DIR = os.path.join(root, 'resources')
app = create_app(config_obj=BaseConfig)
if not (no_browser or debug):
webbrowser.open_new_tab("http://{}:{}".format(host, port))
app.run(host=host, port=port, debug=debug)
def case_obj(ped_lines):
"""Return a test case object with individuals."""
_case = get_cases('tests/fixtures/hapmap.vcf', case_lines=ped_lines)[0]
yield _case
def load(ctx, variant_source, family_file, family_type, root):
"""
Load a variant source into the database.
If no database was found run puzzle init first.
1. VCF: If a vcf file is used it can be loaded with a ped file
2. GEMINI: Ped information will be retreived from the gemini db
"""
root = root or ctx.obj.get('root') or os.path.expanduser("~/.puzzle")
if os.path.isfile(root):
logger.error("'root' can't be a file")
ctx.abort()
logger.info("Root directory is: {}".format(root))
db_path = os.path.join(root, 'puzzle_db.sqlite3')
logger.info("db path is: {}".format(db_path))
if not os.path.exists(db_path):
logger.warn("database not initialized, run 'puzzle init'")
ctx.abort()
if not os.path.isfile(variant_source):
logger.error("Variant source has to be a file")
ctx.abort()
mode = get_file_type(variant_source)
if mode == 'unknown':
logger.error("Unknown file type")
ctx.abort()
#Test if gemini is installed
elif mode == 'gemini':
logger.debug("Initialzing GEMINI plugin")
if not GEMINI:
logger.error("Need to have gemini installed to use gemini plugin")
ctx.abort()
logger.debug('Set puzzle backend to {0}'.format(mode))
variant_type = get_variant_type(variant_source)
logger.debug('Set variant type to {0}'.format(variant_type))
cases = get_cases(
variant_source=variant_source,
case_lines=family_file,
case_type=family_type,
variant_type=variant_type,
variant_mode=mode
)
if len(cases) == 0:
logger.warning("No cases found")
ctx.abort()
logger.info("Initializing sqlite plugin")
store = SqlStore(db_path)
for case_obj in cases:
if store.case(case_obj.case_id) is not None:
logger.warn("{} already exists in the database"
.format(case_obj.case_id))
continue
# extract case information
logger.debug("adding case: {} to puzzle db".format(case_obj.case_id))
store.add_case(case_obj, vtype=variant_type, mode=mode)
def gemini_sv_case_obj(gemini_sv_db_path):
"""Return a case object extracted from gemini database"""
_case = get_cases(gemini_sv_db_path, variant_mode='gemini')[0]
_case['variant_type'] = 'sv'
yield _case
def gemini_case_obj(gemini_db_path):
"""Return a case object extracted from gemini database"""
_case = get_cases(gemini_db_path, variant_mode='gemini')[0]
yield _case
def case_obj(ped_lines):
"""Return a test case object with individuals."""
_case = get_cases('tests/fixtures/hapmap.vcf', case_lines=ped_lines)[0]
yield _case
def view(ctx, host, port, debug, pattern, family_file, family_type,
variant_source, root, no_browser, phenomizer):
"""Visualize DNA variant resources.
1. Look for variant source(s) to visualize and inst. the right plugin
"""
main_loop = (not debug) or (os.environ.get('WERKZEUG_RUN_MAIN') == 'true')
root = root or ctx.obj.get('root') or os.path.expanduser("~/.puzzle")
phenomizer_auth = phenomizer or ctx.obj.get('phenomizer_auth')
BaseConfig.PHENOMIZER_AUTH = True if ctx.obj.get(
'phenomizer_auth') else False
BaseConfig.STORE_ENABLED = True
if variant_source is None:
logger.info("Root directory is: {}".format(root))
db_path = os.path.join(root, 'puzzle_db.sqlite3')
logger.info("db path is: {}".format(db_path))
if not os.path.exists(db_path):
logger.warn("database not initialized, run 'puzzle init'")
ctx.abort()
if os.path.isfile(root):
logger.error("'root' can't be a file")
ctx.abort()
store = SqlStore(db_path, phenomizer_auth=phenomizer_auth)
for case_obj in store.cases():
if case_obj.variant_mode == 'gemini':
if not GEMINI:
logger.error(
"Need to have gemini instaled to view gemini database")
ctx.abort()
else:
logger.info("Using in memory database")
tmpdir = tempfile.mkdtemp()
tmpdb = os.path.join(tmpdir, 'puzzle.sqlite3')
logger.info("building database: {}".format(tmpdb))
store = SqlStore("sqlite:///{}".format(tmpdb),
phenomizer_auth=phenomizer_auth)
if main_loop:
store.set_up()
cases = []
if os.path.isfile(variant_source):
file_type = get_file_type(variant_source)
#Test if gemini is installed
if file_type == 'unknown':
logger.error("File has to be vcf or gemini db")
ctx.abort()
elif file_type == 'gemini':
#Check if gemini is installed
if not GEMINI:
logger.error(
"Need to have gemini installed to use gemini plugin"
)
ctx.abort()
variant_type = get_variant_type(variant_source)
cases = get_cases(variant_source=variant_source,
case_lines=family_file,
case_type=family_type,
variant_type=variant_type,
variant_mode=file_type)
else:
for file in path(variant_source).walkfiles(pattern):
file_type = get_file_type(file)
if file_type != 'unknown':
variant_type = get_variant_type(file)
#Test if gemini is installed
if file_type == 'gemini':
if not GEMINI:
logger.error(
"Need to have gemini installed to use gemini plugin"
)
ctx.abort()
for case in get_cases(variant_source=file,
case_type=family_type,
variant_type=variant_type,
variant_mode=file_type):
cases.append(case)
for case_obj in cases:
if store.case(case_obj.case_id) is not None:
logger.warn("{} already exists in the database".format(
case_obj.case_id))
continue
# extract case information
logger.debug("adding case: {}".format(case_obj.case_id))
store.add_case(case_obj,
vtype=case_obj.variant_type,
mode=case_obj.variant_mode)
logger.debug("Plugin setup was succesfull")
BaseConfig.PUZZLE_BACKEND = store
BaseConfig.UPLOAD_DIR = os.path.join(root, 'resources')
app = create_app(config_obj=BaseConfig)
if no_browser is False:
webbrowser.open_new_tab("http://{}:{}".format(host, port))
app.run(host=host, port=port, debug=debug)