API Reference

Core Modules

class peaktools._cli.CLI[source]

Bases: object

Cli interface for python package peaktools.

  • peaktools is a commandline tool and a python package

reference_point(input, input_bam, output, output_heatmap, output_profile, ref_point='TSS', up_extend_length=3000, down_extend_length=3000, extend_binsize=100, count_norm_method='RPKM', verbose='ERROR', processes=1, temp_dir=None, vmin=0, vmax=None, cmap='Purples')[source]

Calculate matrix and visualize for a reference point.

Parameters:

  • input (str) – Input bed

  • input_bam (str) – Input bam file

  • output (str, optional) – Output csv file.

  • output_heatmap (str, optional) – Output heatmap pdf file.

  • output_profile (str, optional) – Output profile pdf file.

  • up_extend_length (int, optional) – upstream region extend length. Defaults to 3000.

  • down_extend_length (int, optional) – downstream region extend length. Defaults to 3000.

  • extend_binsize (int, optional) – region extend binsize. Defaults to 100.

  • count_norm_method (str, optional) – Can be RPKM, Raw or CPM. Defaults to “RPKM”.

  • verbose (str, optional) – The logging level as a string. Defaults to “ERROR”.

  • processes (int, optional) – Number of processes to use. Defaults to 1.

  • temp_dir (str, optional) – folder to put temp files, use input dir if not defined. Defaults to None.

  • vmin (int, optional) – Lower boundary of scale bar. Defaults to 0.

  • vmax (int, optional) – Upper boundary of scale bar. Defaults to 99% quantile.

  • cmap (str, optional) – Color theme of heatmap. Defaults to “Purples”.

scale_region(input, input_bam, output, output_heatmap, output_profile, up_extend_length=3000, down_extend_length=3000, extend_binsize=100, split_num=100, count_norm_method='RPKM', verbose='ERROR', processes=1, temp_dir=None, vmin=0, vmax=None, cmap='Purples')[source]

Calculate matrix and visualize for a scaled region.

Parameters:

  • input (str) – Input bed

  • input_bam (str) – Input bam file

  • output (str, optional) – Output csv file.

  • output_heatmap (str, optional) – Output heatmap pdf file.

  • output_profile (str, optional) – Output profile pdf file.

  • up_extend_length (int, optional) – upstream region extend length. Defaults to 3000.

  • down_extend_length (int, optional) – downstream region extend length. Defaults to 3000.

  • extend_binsize (int, optional) – region extend binsize. Defaults to 100.

  • split_num (int, optional) – number of bins to split the region. Defaults to 100.

  • count_norm_method (str, optional) – Can be RPKM, Raw or CPM. Defaults to “RPKM”.

  • verbose (str, optional) – The logging level as a string. Defaults to “ERROR”.

  • processes (int, optional) – Number of processes to use. Defaults to 1.

  • temp_dir (str, optional) – folder to put temp files, use input dir if not defined. Defaults to None.

  • vmin (int, optional) – Lower boundary of scale bar. Defaults to 0.

  • vmax (int, optional) – Upper boundary of scale bar. Defaults to 99% quantile.

  • cmap (str, optional) – Color theme of heatmap. Defaults to “Purples”.

peaktools._cli.main()[source]