coalispr.resources.dialog¶

Module for gathering user-input.

Attributes¶

logger

Classes¶

PresentDialog

Present dialog based around given messages.

Functions¶

`assemble_groupsamples`(groups, agroup, trimmings)	Assemble a list of samples to be used by groupcompare.
`collect_limits`(chrnam, rangex)	Collect tuple with coordinates for region to display or, if no
`get_experiment_name`()	Obtain user feedback for name of experiment/session.
`get_old_new_samplenames`(todolist)	Collect tuple with old and new name for a sample in the experiment-file
`select_from`(alist)	Obtain user choice for items from given list.
`suggest_storepath`([path])	Store Coalispr data and configuration files in suggested directory.

Module Contents¶

coalispr.resources.dialog.logger¶

class coalispr.resources.dialog.PresentDialog(msg, item, pattern, per_confirm=True, fcie=None)¶

Present dialog based around given messages.

msg¶

Welcome message

Type:: str

item¶

Requested item

Type:: str

pattern¶

Regular expression to validate user input

Type:: str

per_confirm¶

Flag to use confirm-dialog to verify output

Type:: bool

fcie¶

Function for extra test and that analyzes user input

Type:: function

SKIP = 'skip_this'¶

msg1¶

item¶

pattern¶

stop = 'stop'¶

stopmsg¶

msg2 = Multiline-String¶

Show Value

"""{} will be set to:
          {}
       Is that OK?"""

errortext = Multiline-String¶

Show Value

"""
        Sorry, '{0}' cannot be used. {1}?"""

fcie = None¶

per_confirm = True¶

try_input(commandinput)¶

Check (string) directly given input via the command line.

Parameters:: commandinput (str) – List of input argumnets converted to string that can be parsed by self.fcie and matches pattern.

display_dialog()¶: Show dialog with options.

display_choices(choices, evalas=None)¶

Show choices for doing something.

Parameters:

choices (dir) – Choicename: choice
evalas (str) – alternative string to display

coalispr.resources.dialog.assemble_groupsamples(groups, agroup, trimmings)¶

Assemble a list of samples to be used by groupcompare.

Parameters:

groups (dict of dicts) – Nested dictionaries of samples organized by grouping (from experiment.mixed_groups() )
agroup (str) – Name of chosen group or type to compare samples for.
trimmings (str) – Chosen setting for defining trimming sequence.

Return type:

List of selected items.

coalispr.resources.dialog.collect_limits(chrnam, rangex)¶

Collect tuple with coordinates for region to display or, if no chromosome, a pair of limits setting a range.

Parameters:

chrnam (str) – Name of the chromosome for which the region is returned.
rangex (tuple) – Start and end of region/range to be analyzed.

Returns:

Dialog to gather and return chromosomal coordinates for the region or
a pair of limits.

coalispr.resources.dialog.get_experiment_name()¶: Obtain user feedback for name of experiment/session.

coalispr.resources.dialog.get_old_new_samplenames(todolist)¶

Collect tuple with old and new name for a sample in the experiment-file

Return type:: Dialog to gather and return names for samples.

coalispr.resources.dialog.select_from(alist)¶

Obtain user choice for items from given list.

Parameters:: alist (list) – List of items, or of dicts with items, to choose from.
Return type:: List of selected items.

coalispr.resources.dialog.suggest_storepath(path=None)¶

Store Coalispr data and configuration files in suggested directory.

Parameters:

path (Path) – Location of configuration files (default: None); CONFPATH might not be set properly yet, absent at beginning and needs to be chosen.

Returns:

Local storage folder including sub-folders for data and configuration
templates (‘constant_in’)