Module lib.patterns_targets

The classes in module control how rnaseq_patterns.yaml and chipseq_patterns.yaml are filled in with the information from their respective sample tables and config files.

SeqConfig(config, patterns[, workdir])

This class takes care of common tasks related to config and patterns files (reading the sampletable, etc) but is intended to be subclassed.

RNASeqConfig(config, patterns[, workdir])

Config object specific to RNA-seq workflows.

ChIPSeqConfig(config, patterns[, workdir])

Config object specific to ChIP-seq workflows.

Details

class lib.patterns_targets.SeqConfig(config, patterns, workdir=None)[source]

This class takes care of common tasks related to config and patterns files (reading the sampletable, etc) but is intended to be subclassed.

Parameters:

  • config (str or dict)

  • patterns (str) – Path to patterns YAML file

  • workdir (str) – Config, patterns, and all paths in config should be interpreted as relative to workdir

class lib.patterns_targets.RNASeqConfig(config, patterns, workdir=None)[source]

Config object specific to RNA-seq workflows.

Fills in patterns to create targets by handling the by-sample and by-aggregate sections separately.

Parameters:

  • config (dict)

  • patterns (str) – Path to patterns YAML file

  • workdir (str) – Config, patterns, and all paths in config should be interpreted as relative to workdir

class lib.patterns_targets.ChIPSeqConfig(config, patterns, workdir=None)[source]

Config object specific to ChIP-seq workflows.

Fills in patterns to create targets by handling the by-sample, by-peak, and by-aggregate sections separately.

Parameters:

  • config (dict)

  • patterns (str) – Path to patterns YAML file

  • workdir (str) – Config, patterns, and all paths in config should be interpreted as relative to workdir