RNAmediator.GenerateBigWig.generate_bws

RNAmediator.GenerateBigWig.generate_bws(goi, filelist, chrom, gs, ge, gstrand, ulim, cutoff, border, outdir, padding, chromstr, queue=None, configurer=None, level=None)

Generate BigWig entries

Parameters:

• filelist (list) – List of files to work on

• chrom (str) – Chromosome

• gs (int) – Start coordinate of gene

• ge (int) – End coordinate of gene

• gstrand (str) – Strand of gene

• ulim (int) – Stretch of nucleotides used during plfold run (-u option)

• cutoff (float) – Cutoff for the definition of pairedness, if set to < 1 it will select only constraint regions with mean raw (unconstrained) probability of being unpaired <= cutoff for further processing(default: 1.0)

• border (float) – Cutoff for the minimum change between unconstrained and constraint structure, regions below this cutoff will not be further evaluated.

• outdir (str) – Directory to write to

• padding (int) – Padding around constraint that will be excluded from report, default is 1, so directly overlapping effects will be ignored

• queue (Multiprocessing.Queue, optional) – Queue used for logging process

• configurer (Function, optional) – Function to configure logging

• level (str, optional) – Loglevel