def manage_config(cmd):
"""Manage genomepy config file."""
if cmd == "file":
print(config.config_file)
elif cmd == "show":
with open(config.config_file) as f:
print(f.read())
elif cmd == "generate":
config_dir = user_config_dir("genomepy")
if not os.path.exists(config_dir):
mkdir_p(config_dir)
new_config = os.path.join(config_dir, "genomepy.yaml")
# existing config must be removed before norns picks up the default again
if os.path.exists(new_config):
os.unlink(new_config)
default_config = norns.config("genomepy",
default="cfg/default.yaml").config_file
with open(new_config, "w") as fout, open(default_config) as fin:
fout.write(fin.read())
config.config_file = new_config
print(f"Created config file {new_config}")
else:
raise ValueError(f"Invalid config command: {cmd}")
from bucketcache import Bucket
from pyfaidx import Fasta
from appdirs import user_cache_dir
from genomepy import exceptions
from genomepy.utils import filter_fasta, get_localname
from genomepy.__about__ import __version__
my_cache_dir = os.path.join(user_cache_dir("genomepy"), __version__)
# Create .cache dir if it does not exist
if not os.path.exists(my_cache_dir):
os.makedirs(my_cache_dir)
cached = Bucket(my_cache_dir, days=7)
config = norns.config("genomepy", default="cfg/default.yaml")
class ProviderBase(object):
"""Provider base class.
Use to get a list of available providers:
>>> ProviderBase.list_providers()
['UCSC', 'NCBI', 'Ensembl']
Create a provider:
>>> p = ProviderBase.create("UCSC")
>>> for name, desc in p.search("hg38"):
... print(desc)
Human Dec. 2013 (GRCh38/hg38) Genome at UCSC
"""
import os
import sys
import re
import norns
config = norns.config("genomepy", default="cfg/default.yaml")
class Plugin(object):
"""Plugin base class.
"""
active = False
def name(self):
n = type(self).__name__.replace("Plugin", "")
return convert(n)
def activate(self):
self.active = True
def deactivate(self):
self.active = False
def after_genome_download(self, genome):
raise NotImplementedError("plugin should implement this method")
def get_properties(self, genome):
raise NotImplementedError("plugin should implement this method")
def find_plugins():
"""Locate and initialize all available plugins.
def test_config():
config = norns.config("genomepy", default="cfg/default.yaml")
assert len(config.keys()) == 3
def test_no_arguments():
cfg = norns.config()
def test_basic():
cfg = norns.config(config_file="tests/data/simple.yaml")
assert cfg["integer"] == 10
assert cfg["path"] == "/home/simon"
assert 3 == len(cfg.keys())
