RNAmediator.ConstraintPLFold.constrain_seq_paired

RNAmediator.ConstraintPLFold.constrain_seq_paired(sid, seq, fstart, fend, start, end, window, span, region, temperature, multi, paired, unpaired, save, outdir, constype, consval, unconstrained=None, queue=None, configurer=None, level=None)

Fold Sequences with paired constraint

Parameters:

• sid (str Id for Sequence) –

• seq (str Sequence to fold) –

• fstart (int Start of First subsequence to fold) –

• fend (int End of First subsequence to fold) –

• start (int Start of subsequence to fold) –

• end (int End of subsequence to fold) –

• window (int Size of window to fold) –

• span (int Maximum base-pair span to be evaluated) –

• region (int -u Option of RNAplfold) –

• temperature (float Temperature) –

• multi (int Multiplyer for window extension) –

• paired (str Infix for output files of paired constraint) –

• unpaired (str Infix for ouput files of unpaired constraint) –

• save (bool Should npy or npy and gz output be saved) –

• outdir (str Location of the Outpu directory. If it is an empty string os.cwd() is used) –

• constype (str) – Type of constraint to apply, can be [‘hard’ (Default), ‘soft’(not implemented yet), ‘mutate’]

• consval (str) – Value for constraint to apply, ignored when constype is ‘hard’

• unconstrained (str, optional) – Infix for ouput files of unconstrained folding

• queue (multiprocessing_queue, optional) – Logging process queue

• configurer (multiprocessing_config, optional) – Config for Logging processes

• level (logging.level, optional) – Level for log process

Return type:

Call to write_constraint