RNAmediator.GenerateBigWig.scan_input

RNAmediator.GenerateBigWig.scan_input(queue, configurer, level, pat, cutoff, border, ulim, temperature, procs, unconstrained, unp, pai, outdir, indir, genes, chromsizes, padding, chromstr)

Scan input for files of interest

Parameters:

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

  • configurer (Function) – Function to configure logging

  • level (str) – Loglevel

  • pat (str) – Pattern for and window and span, e.g. 30,250. Window can contain other strings for filtering, e.g. Seq1_30

  • 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.

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

  • temperature (float) – Temperature for structure prediction

  • procs (int) – Number of parallel processes to run this job with

  • unconstrained (str) – Name for unconstrained provided at ConstraintPLFold -r

  • unp (bool) – If unpaired files should be converted as well

  • pai (bool) – If paired files should be converted as well

  • outdir (str) – Directory to write to

  • indir (str) – Directory to read from

  • genes (str) – Genomic coordinates bed for genes in standard BED format

  • chromsizes (str) – Chromosome sizes file

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