Additional utils

class snakemake.utils.AlwaysQuotedFormatter(quote_func=<function quote>, *args, **kwargs)[source]

Subclass of QuotedFormatter that always quotes.

Usage is identical to QuotedFormatter, except that it always acts like “q” was appended to the format spec.

class snakemake.utils.QuotedFormatter(quote_func=<function quote>, *args, **kwargs)[source]

Subclass of string.Formatter that supports quoting.

Using this formatter, any field can be quoted after formatting by appending “q” to its format string. By default, shell quoting is performed using “shlex.quote”, but you can pass a different quote_func to the constructor. The quote_func simply has to take a string argument and return a new string representing the quoted form of the input string.

Note that if an element after formatting is the empty string, it will not be quoted.

snakemake.utils.R(code)[source]

Execute R code

This function executes the R code given as a string. The function requires rpy2 to be installed.

Parameters:code (str) – R code to be executed
class snakemake.utils.SequenceFormatter(separator=' ', element_formatter=<string.Formatter object>, *args, **kwargs)[source]

string.Formatter subclass with special behavior for sequences.

This class delegates formatting of individual elements to another formatter object. Non-list objects are formatted by calling the delegate formatter’s “format_field” method. List-like objects (list, tuple, set, frozenset) are formatted by formatting each element of the list according to the specified format spec using the delegate formatter and then joining the resulting strings with a separator (space by default).

format_element(elem, format_spec)[source]

Format a single element

For sequences, this is called once for each element in a sequence. For anything else, it is called on the entire object. It is intended to be overridden in subclases.

snakemake.utils.available_cpu_count()[source]

Return the number of available virtual or physical CPUs on this system. The number of available CPUs can be smaller than the total number of CPUs when the cpuset(7) mechanism is in use, as is the case on some cluster systems.

Adapted from http://stackoverflow.com/a/1006301/715090

snakemake.utils.format(_pattern, *args, stepout=1, _quote_all=False, **kwargs)[source]

Format a pattern in Snakemake style.

This means that keywords embedded in braces are replaced by any variable values that are available in the current namespace.

snakemake.utils.linecount(filename)[source]

Return the number of lines of given file.

Parameters:filename (str) – the path to the file
snakemake.utils.listfiles(pattern, restriction=None, omit_value=None)[source]

Yield a tuple of existing filepaths for the given pattern.

Wildcard values are yielded as the second tuple item.

Parameters:
  • pattern (str) – a filepattern. Wildcards are specified in snakemake syntax, e.g. “{id}.txt”
  • restriction (dict) – restrict to wildcard values given in this dictionary
  • omit_value (str) – wildcard value to omit
Yields:

tuple – The next file matching the pattern, and the corresponding wildcards object

snakemake.utils.makedirs(dirnames)[source]

Recursively create the given directory or directories without reporting errors if they are present.

snakemake.utils.min_version(version)[source]

Require minimum snakemake version, raise workflow error if not met.

snakemake.utils.read_job_properties(jobscript, prefix='# properties', pattern=re.compile('# properties = (.*)'))[source]

Read the job properties defined in a snakemake jobscript.

This function is a helper for writing custom wrappers for the snakemake –cluster functionality. Applying this function to a jobscript will return a dict containing information about the job.

snakemake.utils.report(text, path, stylesheet='/home/docs/checkouts/readthedocs.org/user_builds/snakemake/checkouts/stable/snakemake/report.css', defaultenc='utf8', template=None, metadata=None, **files)[source]

Create an HTML report using python docutils.

Attention: This function needs Python docutils to be installed for the python installation you use with Snakemake.

All keywords not listed below are intepreted as paths to files that shall be embedded into the document. They keywords will be available as link targets in the text. E.g. append a file as keyword arg via F1=input[0] and put a download link in the text like this:

report('''
==============
Report for ...
==============

Some text. A link to an embedded file: F1_.

Further text.
''', outputpath, F1=input[0])

Instead of specifying each file as a keyword arg, you can also expand
the input of your rule if it is completely named, e.g.:

report('''
Some text...
''', outputpath, **input)
Parameters:
  • text (str) – The “restructured text” as it is expected by python docutils.
  • path (str) – The path to the desired output file
  • stylesheet (str) – An optional path to a css file that defines the style of the document. This defaults to <your snakemake install>/report.css. Use the default to get a hint how to create your own.
  • defaultenc (str) – The encoding that is reported to the browser for embedded text files, defaults to utf8.
  • template (str) – An optional path to a docutils HTML template.
  • metadata (str) – E.g. an optional author name or email address.
snakemake.utils.set_protected_output(*rules)[source]

Set the output of rules to protected

snakemake.utils.set_temporary_output(*rules)[source]

Set the output of rules to temporary

snakemake.utils.simplify_path(path)[source]

Return a simplified version of the given path.

snakemake.utils.update_config(config, overwrite_config)[source]

Recursively update dictionary config with overwrite_config.

See http://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth for details.

Parameters:
  • config (dict) – dictionary to update
  • overwrite_config (dict) – dictionary whose items will overwrite those in config