aggregate_reactivity

ipasuite.workflow.scripts.tools.aggregate_reactivity.aggregate(*files: [<class 'str'>], output: str, refseq: str | None = None, shape_output=None, shape_IP_output=None, map_output=None, relation_output=None, normcol='simple_norm_reactivity', fullplot: str | None = None, plot: str | None = None, plot_title: str | None = None, err_on_dup: bool = True)

Aggregate reactivity files together

Aggregate reactivity between all file in output. Calculate mean and stdev for coherent value of reactivity

Parameters:

• files ([str]) – Files to aggregate together

• output (str) – Output aggregated file

• refseq (str) – Sequence file name

• ipanemap_output – Output aggregated file in a compatible format for RNAFold and IPANEMAP

• normcol – name of the normalization column in each input file

• min_ndata_perc (float) – (default: 0.5) minimum percentage (usable data (not -10)/available data). below this value, data row is discarded

• min_nsubdata_perc (float) – (default: 0.66) When try to find consistant mean on a subsample, this value represent minimum (subsample size / avalaible data). if below this value, data row is discarded

• max_mean_perc (float) – (default: 0.682) in order to be considered as consistant, stdev of a row must be below a certain percentage of mean of the row. max_mean_perc represent this mean percentage.

• min_dispersion (float) – (default: 0.05) the consistancy ratio cannot be below a certain value