snakemake.common package

Subpackages

• snakemake.common.tests package
  • Subpackages
    • snakemake.common.tests.testcases package
      • Subpackages
      • Module contents
  • Module contents

Submodules

snakemake.common.argparse module

class snakemake.common.argparse.ArgumentDefaultsHelpFormatter(prog, indent_increment=2, max_help_position=24, width=None)

Bases: HelpFormatter

Help message formatter which adds default values to argument help.

Like argparse.ArgumentDefaultsHelpFormatter, but doesn’t print None/dataclasses._MISSING_TYPE/etc.

class snakemake.common.argparse.ArgumentGroup(container, title=None, description=None, **kwargs)

Bases: _ArgumentGroup

add_argument(*args, parse_func=None, **kwargs)

This method supports the same args as ArgumentParser.add_argument(..) as well as the additional args below.

Parameters:

• env_var – If set, the value of this environment variable will override any config file or default values for this arg (but can itself be overridden on the commandline). Also, if auto_env_var_prefix is set in the constructor, this env var name will be used instead of the automatic name.

• is_config_file_arg – If True, this arg is treated as a config file path This provides an alternative way to specify config files in place of the ArgumentParser(fromfile_prefix_chars=..) mechanism. Default: False

• is_write_out_config_file_arg – If True, this arg will be treated as a config file path, and, when it is specified, will cause configargparse to write all current commandline args to this file as config options and then exit. Default: False

Returns:

the new argparse action

Return type:

argparse.Action

class snakemake.common.argparse.ArgumentParser(*args, **kwargs)

Bases: ArgumentParser

add_argument(*args, parse_func=None, **kwargs)

This method supports the same args as ArgumentParser.add_argument(..) as well as the additional args below.

Parameters:

• env_var – If set, the value of this environment variable will override any config file or default values for this arg (but can itself be overridden on the commandline). Also, if auto_env_var_prefix is set in the constructor, this env var name will be used instead of the automatic name.

• is_config_file_arg – If True, this arg is treated as a config file path This provides an alternative way to specify config files in place of the ArgumentParser(fromfile_prefix_chars=..) mechanism. Default: False

• is_write_out_config_file_arg – If True, this arg will be treated as a config file path, and, when it is specified, will cause configargparse to write all current commandline args to this file as config options and then exit. Default: False

Returns:

the new argparse action

Return type:

argparse.Action

add_argument_group(*args, **kwargs)

snakemake.common.argparse.register_parser_action(parse_func, kwargs)

snakemake.common.configfile module

snakemake.common.configfile.load_configfile(configpath)

Loads a JSON or YAML configfile as a dict, then checks that it’s a dict.

snakemake.common.git module

snakemake.common.git.get_git_root(path)

Parameters:

path – (str) Path a to a directory/file that is located inside the repo

Returns:

path to the root folder for git repo

snakemake.common.git.get_git_root_parent_directory(path, input_path)

This function will recursively go through parent directories until a git repository is found or until no parent directories are left, in which case an error will be raised. This is needed when providing a path to a file/folder that is located on a branch/tag not currently checked out.

Parameters:

• path – (str) Path a to a directory that is located inside the repo

• input_path – (str) origin path, used when raising WorkflowError

Returns:

path to the root folder for git repo

snakemake.common.git.git_content(git_file)

This function will extract a file from a git repository, one located on the filesystem. The expected format is git+file:///path/to/your/repo/path_to_file@version

Parameters:

env_file (str) – consist of path to repo, @, version, and file information Ex: git+file:///home/smeds/snakemake-wrappers/bio/fastqc/wrapper.py@0.19.3

Returns:

file content or None if the expected format isn’t meet

snakemake.common.git.split_git_path(path)

snakemake.common.tbdstring module

class snakemake.common.tbdstring.TBDString(_=None)

Bases: str

snakemake.common.typing module

snakemake.common.workdir_handler module

class snakemake.common.workdir_handler.WorkdirHandler(workdir=None)

Bases: object

change_back()

change_to()

olddir: Optional[Path] = None

workdir: Optional[Path] = None

Module contents

class snakemake.common.Gather

Bases: object

A namespace for gather to allow items to be accessed via dot notation.

class snakemake.common.Rules

Bases: object

A namespace for rules so that they can be accessed via dot notation.

class snakemake.common.Scatter

Bases: object

A namespace for scatter to allow items to be accessed via dot notation.

snakemake.common.async_run(coroutine)

Attaches to running event loop or creates a new one to execute a coroutine. .. seealso:

https://github.com/snakemake/snakemake/issues/1105
https://stackoverflow.com/a/65696398

snakemake.common.bytesto(bytes, to, bsize=1024)

convert bytes to megabytes. bytes to mb: bytesto(bytes, ‘m’) bytes to gb: bytesto(bytes, ‘g’ etc. From https://gist.github.com/shawnbutts/3906915

snakemake.common.copy_permission_safe(src, dst)

Copy a file to a given destination.

If destination exists, it is removed first in order to avoid permission issues when the destination permissions are tried to be applied to an already existing destination.

snakemake.common.dict_to_key_value_args(some_dict, quote_str=True, repr_obj=False)

snakemake.common.expand_vars_and_user(value)

snakemake.common.get_appdirs()

snakemake.common.get_container_image()

snakemake.common.get_file_hash(filename, algorithm='sha256')

find the SHA256 hash string of a file. We use this so that the user can choose to cache working directories in storage.

snakemake.common.get_function_params(func)

snakemake.common.get_input_function_aux_params(func, candidate_params)

snakemake.common.get_last_stable_version()

snakemake.common.get_report_id(path)

Return type:

str

snakemake.common.get_snakemake_searchpaths()

snakemake.common.get_uuid(name)

snakemake.common.group_into_chunks(n, iterable)

Group iterable into chunks of size at most n.

See https://stackoverflow.com/a/8998040.

snakemake.common.is_local_file(path_or_uri)

snakemake.common.is_namedtuple_instance(x)

snakemake.common.log_location(msg)

snakemake.common.mb_to_mib(mb)

snakemake.common.num_if_possible(s)

Convert string to number if possible, otherwise return string.

snakemake.common.overwrite_function_params(func, params)

Force function params to be the given list. Useful for functions that use *args to get all parameters in dynamically created cases like in snakemake.ioutils.subpath.subpath.

snakemake.common.parse_key_value_arg(arg, errmsg, strip_quotes=True)

snakemake.common.parse_uri(path_or_uri)

snakemake.common.set_env(**environ)

Temporarily set the process environment variables.

>>> with set_env(PLUGINS_DIR='test/plugins'):
...   "PLUGINS_DIR" in os.environ
True

>>> "PLUGINS_DIR" in os.environ
False

Parameters:

environ (Dict[str, unicode]) – Environment variables to set

snakemake.common.smart_join(base, path, abspath=False)

snakemake.common.strip_prefix(text, prefix)

snakemake.common.unique_justseen(iterable, key=None)

List unique elements, preserving order. Remember only the element just seen.

From https://docs.python.org/3/library/itertools.html#itertools-recipes