hts.protocol package

Submodules

hts.protocol.protocol module

synopsis

The Protocol Class.

class hts.protocol.protocol.Protocol(file, name, tasks, config)[source]

Bases: object

Protocol describes all information connected to the protocol of a high throughput screen.

file

File name of the protocol file.

Type

str

name

Name of the protocol

Type

str

tasks

List of Protocol Tasks

Type

list of ProtocolTasks

classmethod create(path, format=None)[source]

Create Protocol instance.

Create Protocol instance.

Parameters

  • path (str) – Path to input file or directory

  • format (str) – Format of the input file, at current not specified

get_tasks_by_tag(tag)[source]
write(format, path=None, return_string=None, *args)[source]

Serialize and write Protocol instances.

Serialize Protocol instance using the stated format.

Parameters

  • format (str) – The output format: Currently only “pickle”.

  • path (str) – Path to output file

Todo

Write checks for format and path.

class hts.protocol.protocol.ProtocolTask(name, tags, type, method, config)[source]

Bases: object

ProtocolTask describes all information connected to a task defined in a protocol of a high throughput screen.

name

Name of the task

Type

str

tags

List of all tags of this Task. Necessarily needs to include exactly one of KNOWN_TASK_TYPES

Type

list of str

type

One of KNOWN_TASK_TYPES

Type

str

method

(str): Name of a method in type.

config

(configobj.ConfigObj): configobj.ConfigObj

classmethod create(name, config)[source]

Create ProtocolTask instance.

Create ProtocolTask instance.

Parameters

  • name (str) – The arbitrary name of the protocol task

  • config (ConfigObj) – ConfigObj

Module contents