util

class anadama2.util.Bag

class anadama2.util.Directory(name)

create()

exists()

files(pattern=None)

class anadama2.util.HasNoEqual

class anadama2.util.SerializableMixin

Mixin that defines a few methods to simplify serializing objects

serializable_attrs = []

exception anadama2.util.SerializationError

exception anadama2.util.ShellException

exception anadama2.util.SparseMetadataException

anadama2.util.capture(*args, **kwds)

anadama2.util.deserialize(s=None, from_fp=None)

anadama2.util.deserialize_csv(file_handle)

anadama2.util.deserialize_map_file(file_handle)

Returns a list of namedtuples according to the contents of the file_handle according to the customs of QIIME

anadama2.util.dichotomize(it, tf_func)

Split an iterable into two lists by use of a function that returns True or False.

Parameters:

• it – The items to split
• tf_func – A function that returns True or False

Returns:

2-Tuple of lists: the items for which the function returned True, and the items for which the function returned False

anadama2.util.dict_to_cmd_opts(*args, **kwds)

anadama2.util.dict_to_cmd_opts_iter(opts_dict, shortsep=' ', longsep='=', shortdash='-', longdash='--')

sep separates long options and their values, singlesep separates short options and their values e.g. –long=foobar vs -M 2

anadama2.util.filter_compressed(fname_list)

Return only files that are known to be compressed and in a recognized compression format

anadama2.util.find_on_path(*args, **kwargs)

Finds an executable living on the shells PATH variable. :param bin_str: String; executable to find

Returns:Absolute path to bin_str or False if not found Return type:str

anadama2.util.first(iterable)

anadama2.util.generator_flatten(gen)

anadama2.util.get_name(t)

Get the name of a tracked object

Parameters:t (objects implementing the anadama2.tracked.Base interface) – The tracked object

anadama2.util.guess_seq_filetype(guess_from)

anadama2.util.intatleast1(n)

anadama2.util.is_compressed(fname)

anadama2.util.islambda(func)

anadama2.util.isnottask(x)

anadama2.util.istask(x)

anadama2.util.kebab(s)

Kebab-case a string. Intra-string whitespace is converted to - and unfriendly characters are dropped.

anadama2.util.keepkeys(d, keys)

Drop all keys from dictionary d except those in keys. Modifies the dictionary in place!

Parameters:

• d (dict) – The dictionary to modify
• keys (iterable) – The keys to keep

anadama2.util.keyrename(d, mapping)

Change all keys in dictionary d according to mapping. Modifies d in place!

Parameters:

• d (dict) – The dictionary to change
• mapping (iterable of 2-tuples) – The keys to change and to what to change them

anadama2.util.memoized(func)

anadama2.util.mkdirp(path)

anadama2.util.noop(*args, **kwargs)

anadama2.util.partition(it, binsize, pad=None)

anadama2.util.serialize(obj, to_fp=None)

anadama2.util.serialize_map_file(namedtuples, output_fname)

anadama2.util.sh(cmd, **kwargs)

anadama2.util.sugar_list(x)

Turns just a single thing into a list containing that single thing.

anadama2.util.take(raw_seq_files, index_list)

anadama2.util.underscore(s, repl='[\\s/:@\\, *?]+')

Remove all whitespace and replace with underscores

anadama2.util.which_compressed_idxs(fname_mtx)