class ArgFiller

class rnaseqflow.cliutils.ArgFiller(args)

An interactive method of filling in arguments not given at runtime

Code completion taken from https://gist.github.com/iamatypeofwalrus/5637895

_fill_adapters()

Fill in self.args.adapters with a valid file path

_fill_blocksize()

Fill in self.args.blocksize with a valid integer (in kB)

_fill_ext()

Fill in self.args.ext with a file type extension

_fill_fastq()

Fill in the fastq-mcf executable self.args.fastq with a default 'fastq-mcf'

_fill_fastq_args()

Fill in self.args.fastq_args

_fill_quiet()

Fill in the quiet argument self.args.quiet with default False

_fill_root()

Fill in self.args.root with a valid root directory

classmethod _get_directory_input(message)

Ask the user to enter a directory path in the command line

Parameters:message (str) -- a message to display with raw_input

classmethod _get_filepath_input(message)

Ask the user to enter a file path in the command line

Parameters:message (str) -- a message to display with raw_input

classmethod _get_integer_input(message)

Ask the user to enter an integer in the command line

Parameters:message (str) -- a message to display with raw_input

fill(args_needed)

Add the needed arguments to self.args if they are not there

Asks the user for input for each of the missing arguments

Parameters:args_needed (list(str)) -- a list of attributes to ensure self.args contains

pathCompleter(text, state)

This is the tab completer for systems paths.

set_path_complete(enable)

Enable or disable readline pathcompletion

Parameters:enable (bool) -- enable or disable completion

function all_subclasses

rnaseqflow.cliutils.all_subclasses(cls)

Recursively generate all subclasses of cls

Parameters:cls -- a python class Returns:all subclasses of cls Return type:list(cls)

function trim

rnaseqflow.cliutils.trim(docstring)

Trim a PEP 0257 docstring

Code taken directly from PEP 0257#handling-docstring-indentation

Parameters:docstring (str) -- a Python docstring Returns:the first line of the docstring Return type:str

function firstline

rnaseqflow.cliutils.firstline(docstring)

Extract and return only the first line of a PEP 0257 docstring

Parameters:docstring (str) -- a Python docstring Returns:the first line of the docstring Return type:str