stats module

class mavis.bam.stats.BamStats(median_fragment_size, stdev_fragment_size, read_length)

Bases: object

add_stranded_information(strand_hist)

class mavis.bam.stats.Histogram

Bases: dict

__add__(other)

sum two histograms and return the result as a new histogram

Example

>>> x, y = Histogram(), Histogram()
>>> x.add('item')
>>> y.add('item')
>>> x + y
{'item': 2}

add(item, freq=1)

add a key to the histogram with a default frequency of 1

distribution_stderr(median, fraction, error_function=<function Histogram.<lambda>>)

median()

flattens the histogram to compute the median value

mavis.bam.stats.compute_genome_bam_stats(bam_file_handle, sample_bin_size, sample_size, log=<function devnull>, min_mapping_quality=1, sample_cap=10000, distribution_fraction=0.99)

computes various statistical measures relating the input bam file

Parameters:

• bam_file_handle (pysam.AlignmentFile) – the input bam file handle
• sample_bin_size (int) – how large to make the sample bin (in bp)
• sample_size (int) – the number of genes to compute stats over
• log (callable) – outputs logging information
• min_mapping_quality (int) – the minimum mapping quality for a read to be used
• sample_cap (int) – maximum number of reads to collect for any given sample region
• distribution_fraction (float) – the proportion of the distribution to use in computing stdev

Returns:

the fragment size median, stdev and the read length in a object

Return type:

BamStats

mavis.bam.stats.compute_transcriptome_bam_stats(bam_file_handle, annotations, sample_size, log=<function devnull>, min_mapping_quality=1, stranded=True, sample_cap=10000, distribution_fraction=0.97)

computes various statistical measures relating the input bam file

Parameters:

• bam_file_handle (pysam.AlignmentFile) – the input bam file handle
• annotations (object) – see load_reference_genes()
• sample_size (int) – the number of genes to compute stats over
• log (callable) – outputs logging information
• min_mapping_quality (int) – the minimum mapping quality for a read to be used
• stranded (bool) – if True then reads must match the gene strand
• sample_cap (int) – maximum number of reads to collect for any given sample region
• distribution_fraction (float) – the proportion of the distribution to use in computing stdev

Returns:

the fragment size median, stdev and the read length in a object

Return type:

BamStats