API Reference¶
-
snakescale.
scale
(tool: str, subtool: Optional[str] = None, version: str = 'latest', as_uri: bool = True) → str[source]¶
-
snakescale.formatters.
clean_picard_style_value
(value: Union[List[str], str]) → Union[List[str], str][source]¶ Clean a dictionary of Picard key-value pairs.
-
snakescale.formatters.
snakecase_to_kebab_case
(key: str) → str[source]¶ Convert snake_case to kebab-case.
-
snakescale.formatters.
format_bedtools_params
(params: Mapping) → str[source]¶ Clean a dictionary of bedtools key-value pairs.
-
snakescale.formatters.
format_bwa_params
(params: Mapping) → str[source]¶ Clean a dictionary of bwa key-value pairs.
-
snakescale.formatters.
format_dwgsim_params
(params: Mapping) → str[source]¶ Clean a dictionary of dwgsim key-value pairs.
-
snakescale.formatters.
format_fgbio_params
(params: Mapping) → str[source]¶ Clean a dictionary of fgbio key-value pairs.
-
snakescale.formatters.
format_kraken_params
(params: Mapping) → str[source]¶ Clean a dictionary of kraken key-value pairs.
-
snakescale.formatters.
format_picard_params
(params: Mapping) → str[source]¶ Clean a dictionary of picard key-value pairs.
-
snakescale.resources.
collect_jvm_resources
() → str[source]¶ Collect JVM resources allocations the resource dictionary.
-
snakescale.resources.
collect_picard_style_jvm_resources
() → str[source]¶ Collect Picard specific JVM resources allocations the resource dictionary.
-
class
snakescale.utils.
ExitCode
[source]¶ Bases:
int
The code returned to a parent process by an executable.
Examples
>>> from subprocess import call >>> exit_code = ExitCode(call('ls')) >>> exit_code.is_ok() True
-
class
snakescale.utils.
ProcessReturn
[source]¶ Bases:
tuple
A collection of STDOUT, STDERR, and exit code from a terminated process.
-
stdout
¶ Alias for field number 0
-
stderr
¶ Alias for field number 1
-
exit_code
¶ Alias for field number 2
-
_asdict
()¶ Return a new OrderedDict which maps field names to their values.
-
classmethod
_make
(iterable, new=<built-in method __new__ of type object at 0x886c00>, len=<built-in function len>)¶ Make a new ProcessReturn object from a sequence or iterable
-
_replace
(**kwds)¶ Return a new ProcessReturn object replacing specified fields with new values
-
-
snakescale.utils.
call_snakemake
(arguments: str) → snakescale.utils.ProcessReturn[source]¶ Call Snakemake in this thread as if we are using the CLI.
Parameters: arguments – A string of arguments to pass to Snakemake. Examples
>>> process_return = call_snakemake('') >>> process_return.exit_code.is_ok() False >>> process_return.stderr.strip() 'Error: Snakefile "Snakefile" not present.'