trtools.qcSTR module

trtools.qcSTR.OutputChromCallrate(chrom_calls, fname)

Plot number of calls per chromosome

Parameters

  • chrom_calls (dict of str->int) – Number of calls for each chromosome

  • fname (str) – Filename of output plot

trtools.qcSTR.OutputDiffRefBias(diffs_from_ref, reflens, fname, xlim=(0, 100), mingts=100, metric='mean', binsize=5)

Plot reflen vs. mean difference from ref bias plot

Parameters

  • diffs_from_ref (list of int) – Difference of each allele call from the ref allele (in bp)

  • reflens (list of int) – List of reference allele lengths for each call (in bp)

  • fname (str) – Filename of output plot

  • xlim (tuple of int, optional) – Specify the minimum and maximum x-axis range (in bp)

  • mingts (int, optional) – Don’t plot data points computed based on fewer than this many genotypes

  • metric (str, optional) – Which metric to plot on the y-axis value. Must be mean or median

  • binsize (int, optional) – Size (in bp) of bins on the x-axis.

trtools.qcSTR.OutputDiffRefHistogram(diffs_from_ref, fname)

Plot histogram of difference in bp from reference allele

Parameters

  • diffs_from_ref (list of int) – Difference of each allele call from the ref allele (in units)

  • fname (str) – Filename of output plot

trtools.qcSTR.OutputQualityLocusStrat(per_call_data, loci, fname)

Plot quality of calls, one line for each locus

Parameters

  • per_call_data (numpy.ndarray) – 2D array of qualities of calls where each row is a locus and each col is a sample.

  • loci (List[str]) – List of the IDs of loci

  • fname (str) – Location to save the output plot

trtools.qcSTR.OutputQualityPerCall(per_call_data, fname)

Plot quality of calls as one distribution, irrespective of which sample or locus they came from.

Parameters

  • per_call_data (numpy.ndarray) – 1D array of the qualities of all calls

  • fname (str) – Location to save the output plot

trtools.qcSTR.OutputQualityPerLocus(per_locus_data, fname)

Plot quality of calls per locus

Parameters

  • per_locus_data (numpy.ndarray) – 1D array of an average quality for each locus, defined as the average of qualities of calls across all samples at that locus

  • fname (str) – Location to save the output plot

trtools.qcSTR.OutputQualityPerSample(per_sample_data, fname)

Plot quality of calls per sample

Parameters

  • per_sample_data (numpy.ndarray) – 1D array of the average quality for each sample, defined as the average of qualities of calls across all loci at that sample

  • fname (str) – Location to save the output plot

trtools.qcSTR.OutputQualitySampleStrat(per_call_data, samples, fname)

Plot quality of calls, one line for each sample

Parameters

  • per_call_data (numpy.ndarray) – 2D array of qualities of calls where each row is a locus and each col is a sample.

  • samples (List[str]) – List of the names of samples

  • fname (str) – Location to save the output plot

trtools.qcSTR.OutputSampleCallrate(sample_calls, samples, fname)

Plot number of calls per sample

Parameters

  • sample_calls (numpy.ndarray) – 1D array, number of calls for each sample

  • samples (List[str]) – List of names of samples, same len as sample_calls

  • fname (str) – Filename of output plot

trtools.qcSTR.getargs()
trtools.qcSTR.main(args)
trtools.qcSTR.run()