Index

_

__init__() (RNAmediator.risvis.DataStore method) (RNAmediator.Tweaks.RNAmediator.Constraint method) (RNAmediator.Tweaks.RNAmediator.SequenceSettings method) (RNAmediator.Tweaks.RNAtweaks.FoldOutput method) (RNAmediator.Tweaks.RNAtweaks.PLFoldOutput method)

A

add_chrstr() (in module RNAmediator.GenerateBigWig) add_constraints() (RNAmediator.Tweaks.RNAmediator.SequenceSettings method) add_rnamediator_constraint() (in module RNAmediator.Tweaks.RNAmediator) annotate() (RNAmediator.Tweaks.RNAtweaks.FoldOutput method)

api_rnafold() (in module RNAmediator.Tweaks.RNAtweaks) api_rnaplfold() (in module RNAmediator.Tweaks.RNAtweaks) apply_args_and_kwargs() (in module RNAmediator.CollectConsResults) (in module RNAmediator.GenerateBigWig)

B

backup() (in module RNAmediator.Tweaks.FileProcessor)

bpp_callback() (in module RNAmediator.Tweaks.RNAtweaks)

C

calc() (in module RNAmediator.CollectWindowResults) calcdiff() (in module RNAmediator.CollectWindowDiffs) check_raw_existing() (in module RNAmediator.ConstraintPLFold) check_run() (in module RNAmediator.Tweaks.Collection) checkexisting() (in module RNAmediator.ConstraintFold) (in module RNAmediator.ConstraintPLFold) checklog() (in module RNAmediator.Tweaks.logger) cmd_rnafold() (in module RNAmediator.Tweaks.RNAtweaks) cmd_rnaplfold() (in module RNAmediator.Tweaks.RNAtweaks)

constrain_seq() (in module RNAmediator.ConstraintFold) (in module RNAmediator.ConstraintPLFold) constrain_seq_paired() (in module RNAmediator.ConstraintPLFold) constrain_temp() (in module RNAmediator.ConstraintFold) constrainlist (RNAmediator.Tweaks.RNAmediator.SequenceSettings property) Constraint (class in RNAmediator.Tweaks.RNAmediator) constraintype (RNAmediator.Tweaks.RNAmediator.SequenceSettings property) convertcol() (in module RNAmediator.Tweaks.NPtweaks) create_bw_entries() (in module RNAmediator.GenerateBigWig)

D

DataStore (class in RNAmediator.risvis)

E

equalize_lists() (in module RNAmediator.GenerateBigWig) expand_pl_window() (in module RNAmediator.Tweaks.RNAmediator)

expand_window() (in module RNAmediator.Tweaks.Collection) (in module RNAmediator.Tweaks.RNAmediator)

F

fill_array() (in module RNAmediator.GenerateBigWig) fold() (in module RNAmediator.ConstraintFold) fold_unconstraint() (in module RNAmediator.ConstraintFold) (in module RNAmediator.ConstraintPLFold) foldaround() (in module RNAmediator.ConstraintFold)

FoldOutput (class in RNAmediator.Tweaks.RNAtweaks) from_file() (RNAmediator.Tweaks.RNAtweaks.PLFoldOutput class method) from_numpy() (RNAmediator.Tweaks.RNAtweaks.PLFoldOutput class method) from_RNAfold_file() (RNAmediator.Tweaks.RNAtweaks.FoldOutput class method) from_rnamediator_fold_compound() (RNAmediator.Tweaks.RNAtweaks.FoldOutput method) from_rnamediator_numpy_output() (RNAmediator.Tweaks.RNAtweaks.PLFoldOutput class method)

G

generate_bws() (in module RNAmediator.GenerateBigWig) get_chunks() (in module RNAmediator.CollectConsResults) get_gene_coords() (in module RNAmediator.Tweaks.RNAmediator) get_location() (in module RNAmediator.Tweaks.Collection) (in module RNAmediator.Tweaks.RNAtweaks) get_location_withchrom() (in module RNAmediator.Tweaks.RNAtweaks) get_rnamediator_np_array() (RNAmediator.Tweaks.RNAtweaks.PLFoldOutput method)

get_text() (RNAmediator.Tweaks.RNAtweaks.FoldOutput method) (RNAmediator.Tweaks.RNAtweaks.PLFoldOutput method) getfiles() (in module RNAmediator.GenerateBigWig) gethighest_dict() (in module RNAmediator.Tweaks.DStweaks) gethighest_list() (in module RNAmediator.Tweaks.DStweaks) getlowest_dict() (in module RNAmediator.Tweaks.DStweaks) getlowest_list() (in module RNAmediator.Tweaks.DStweaks)

I

idfromfa() (in module RNAmediator.Tweaks.FileProcessor)

isinvalid() (in module RNAmediator.Tweaks.Collection) isvalid() (in module RNAmediator.Tweaks.Collection)

J

judge_diff() (in module RNAmediator.CollectConsResults)

L

listener_configurer() (in module RNAmediator.Tweaks.logger) listener_process() (in module RNAmediator.Tweaks.logger) localize() (RNAmediator.Tweaks.RNAtweaks.PLFoldOutput method)

localize_pl_window() (in module RNAmediator.Tweaks.RNAmediator) localize_window() (in module RNAmediator.Tweaks.Collection) (in module RNAmediator.Tweaks.RNAmediator)

M

main() (in module RNAmediator.CollectConsResults) (in module RNAmediator.CollectWindowDiffs) (in module RNAmediator.CollectWindowResults) (in module RNAmediator.ConstraintFold) (in module RNAmediator.ConstraintPLFold) (in module RNAmediator.GenerateBigWig) make_outdir() (in module RNAmediator.Tweaks.FileProcessor) makelogdir() (in module RNAmediator.Tweaks.logger) makelogfile() (in module RNAmediator.Tweaks.logger) makeoutdir() (in module RNAmediator.Tweaks.Collection) merge_dicts() (in module RNAmediator.Tweaks.Collection) module RNAmediator RNAmediator.CollectConsResults RNAmediator.CollectWindowDiffs RNAmediator.CollectWindowResults RNAmediator.ConstraintFold RNAmediator.ConstraintPLFold RNAmediator.GenerateBigWig RNAmediator.risvis RNAmediator.Tweaks RNAmediator.Tweaks.Collection RNAmediator.Tweaks.DStweaks RNAmediator.Tweaks.FileProcessor RNAmediator.Tweaks.logger RNAmediator.Tweaks.NPtweaks RNAmediator.Tweaks.Plots RNAmediator.Tweaks.RNAmediator RNAmediator.Tweaks.RNAmediatorArgparsers RNAmediator.Tweaks.RNAtweaks

N

numpy_array (RNAmediator.Tweaks.RNAtweaks.PLFoldOutput property)

O

on_error() (in module RNAmediator.Tweaks.Collection)

P

parse_anno() (RNAmediator.Tweaks.RNAtweaks.FoldOutput method) parse_annotation_bed() (in module RNAmediator.Tweaks.FileProcessor) parse_annotation_bed_by_coordinates() (in module RNAmediator.Tweaks.FileProcessor) parseargs() (in module RNAmediator.risvis) parseargs_browser() (in module RNAmediator.Tweaks.RNAmediatorArgparsers) parseargs_collect_window() (in module RNAmediator.Tweaks.RNAmediatorArgparsers) parseargs_collect_windowdiff() (in module RNAmediator.Tweaks.RNAmediatorArgparsers) parseargs_collectpl() (in module RNAmediator.Tweaks.RNAmediatorArgparsers) parseargs_foldcons() (in module RNAmediator.Tweaks.RNAmediatorArgparsers)

parseargs_plcons() (in module RNAmediator.Tweaks.RNAmediatorArgparsers) parseseq() (in module RNAmediator.Tweaks.FileProcessor) pl_fold() (in module RNAmediator.ConstraintPLFold) PLFoldOutput (class in RNAmediator.Tweaks.RNAtweaks) plot_data() (in module RNAmediator.Tweaks.Plots) plot_temp() (in module RNAmediator.Tweaks.Plots) preprocess() (in module RNAmediator.Tweaks.RNAmediator) print_globaldicts() (in module RNAmediator.Tweaks.Collection) print_globallists() (in module RNAmediator.Tweaks.Collection) printdiff() (in module RNAmediator.Tweaks.RNAtweaks)

R

read_chromsize() (in module RNAmediator.GenerateBigWig) read_constraints() (in module RNAmediator.Tweaks.RNAmediator) read_constraints_from_bed() (in module RNAmediator.Tweaks.FileProcessor) read_constraints_from_csv() (in module RNAmediator.Tweaks.FileProcessor) read_constraints_from_generic() (in module RNAmediator.Tweaks.FileProcessor) read_paired_constraints_from_bed() (in module RNAmediator.Tweaks.FileProcessor) readData() (in module RNAmediator.risvis) rec_dd() (in module RNAmediator.GenerateBigWig) removekey() (in module RNAmediator.Tweaks.DStweaks) RNAmediator module RNAmediator.CollectConsResults module RNAmediator.CollectWindowDiffs module RNAmediator.CollectWindowResults module RNAmediator.ConstraintFold module RNAmediator.ConstraintPLFold module RNAmediator.GenerateBigWig module

RNAmediator.risvis module RNAmediator.Tweaks module RNAmediator.Tweaks.Collection module RNAmediator.Tweaks.DStweaks module RNAmediator.Tweaks.FileProcessor module RNAmediator.Tweaks.logger module RNAmediator.Tweaks.NPtweaks module RNAmediator.Tweaks.Plots module RNAmediator.Tweaks.RNAmediator module RNAmediator.Tweaks.RNAmediatorArgparsers module RNAmediator.Tweaks.RNAtweaks module rnamediator_logging_setup() (in module RNAmediator.Tweaks.RNAmediator)

S

savelists() (in module RNAmediator.CollectConsResults) scan_input() (in module RNAmediator.GenerateBigWig) scan_seq() (in module RNAmediator.ConstraintPLFold) screen_diffs() (in module RNAmediator.CollectWindowDiffs) screen_genes() (in module RNAmediator.CollectConsResults) (in module RNAmediator.CollectWindowResults) SequenceSettings (class in RNAmediator.Tweaks.RNAmediator)

serve() (in module RNAmediator.risvis) set_constraintype() (RNAmediator.Tweaks.RNAmediator.SequenceSettings method) set_run_settings_dict() (in module RNAmediator.Tweaks.RNAmediator) setup_logger() (in module RNAmediator.Tweaks.logger) sortout() (in module RNAmediator.GenerateBigWig) starmap_with_kwargs() (in module RNAmediator.CollectConsResults) (in module RNAmediator.GenerateBigWig)

T

toarray() (in module RNAmediator.Tweaks.NPtweaks)

V

visualiziation_parser() (in module RNAmediator.Tweaks.RNAmediatorArgparsers)

W

worker() (in module RNAmediator.Tweaks.logger) worker_configurer() (in module RNAmediator.Tweaks.logger) write_constraint() (in module RNAmediator.ConstraintPLFold) write_out() (in module RNAmediator.CollectWindowDiffs) (in module RNAmediator.CollectWindowResults) (in module RNAmediator.ConstraintFold)

write_unconstraint() (in module RNAmediator.ConstraintPLFold) writebws() (in module RNAmediator.GenerateBigWig)