RNAmediator.Tweaks.RNAmediator

Functions

add_rnamediator_constraint(run_settings, ...)	Adds constraints in string format to the goi in the run settings dict.
expand_pl_window(start, end, window, ...)
expand_window(start, end, window[, seqlen, dist])
get_gene_coords(genecoords, goi, strand)	Get genomic coordinates for a gene (goi) from the genecoords dict or returns default values
localize_pl_window(start, end, window, seqlen)
localize_window(start, end, tostart, toend)
preprocess(sequence, constraint, conslength, ...)	builds the run settings dict and creates the output directory
read_constraints(constraint[, linewise, ...])	Reads constraints from the constraints file
rnamediator_logging_setup(logdir, loglevel, ...)	creates log process, queue, config, dir and file according to runscript
set_run_settings_dict(sequence, constraint, ...)	Use command line parameters to build the run settings dictionary.

Classes

Constraint(start, end, strand[, value])
SequenceSettings(sequence_record[, gene, ...])	Constraint(PL)fold settings for a sequence object.