RNAmediator.ConstraintFold.constrain_seq

RNAmediator.ConstraintFold.constrain_seq(seq_record, const, conslength, cons, window, span, temp, save='STDOUT', outdir=None, genecoords=None, queue=None, configurer=None, level=None)

takes input of fold and folds constrained and unconstrained sequences

Parameters:

  • seq_record (SeqIO.SeqRecord Sequence record of the sequence to which the constraint should be added) –

  • const (list The constraint position(s) as list) –

  • conslength (int Length of the constraint, only used if constrain is sliding) –

  • cons (str The constraint annotation) –

  • window (int Size of window to fold) –

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

  • temp (int) – Temperature to fold at

  • save (str) – If not STDOUT will be saved to file

  • outdir (str Location for the output directory) –

  • genecoords (list Genomic coordinates of gene of interest) –

  • procs (int Number of processes to run in parallel) –

  • queue (multiprocessing_queue Logging process queue) –

  • configurer (multiprocessing_config for Logging processes) –

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

Return type:

Call to writeout which prints results to file