bsxplorer 1.0.0rc5

Analytical framework for BS-seq data comparison and visualization

BSXplorer

Analytical framework for BS-seq data comparison and visualization.

For Python API reference manual and tutorials visit: https://shitohana.github.io/BSXplorer.

Installation

pip install bsxplorer

Console usage

• bsxplorer-metagene - Create Metagene report
• bsxplorer-category - Categorize regions by P_cg metric and render HTML-report
• bsxplorer-chr - Visualize chromosome methylation levels and render HTML-report

Config file

All console scripts require configuration file – tab separated file with columns:

Column NAMES should NOT be INCLUDED in real configuration file.

Group name	Path to report	Path to annotation	Flank length	Min region length	Genome type	Report type
Mock	mock-1.CX_report.txt	annotation.gff	2000	0	gff	bismark
Mock	mock-2.CX_report.txt	annotation.gff	2000	0	gff	bismark
Infected	infected-1.CX_report.txt	annotation.gff	2000	0	gff	bismark
Infected	infected-2.CX_report.txt	annotation.gff	2000	0	gff	bismark

Columns with underlined are required.

Currently only gff genome_type and only bismark report_type are supported in colsole version of BSXplorer, although you still can read various formats from Python API.

bsxplorer-metagene

bsxplorer-metagene --help
                                                                                   
usage: BSXplorer [-h] [-o NAME] [--dir DIR] [-m BLOCK_MB] [-t] [-s {wmean,mean,median,min,max,1pgeom}] [-u UBIN] [-d DBIN] [-b BBIN] [-q QUANTILE] [-C CONFIDENCE] [-S SMOOTH] [-H VRESOLUTION] [-V HRESOLUTION]
                 [--separate_strands] [--export {pdf,svg,none}] [--ticks TICKS TICKS TICKS TICKS TICKS]
                 config

Metagene report creation tool

positional arguments:
  config                Path to config file

optional arguments:
  -h, --help            show this help message and exit
  -o NAME, --out NAME   Output filename (default: Metagene_Report_12-02-24_10-48-20)
  --dir DIR             Output and working dir (default: $CWD)
  -m BLOCK_MB, --block_mb BLOCK_MB
                        Block size for reading. (Block size ≠ amount of RAM used. Reader allocates approx. Block size * 20 memory for reading.) (default: 50)
  -t, --threads         Do multi-threaded or single-threaded reading. If multi-threaded option is used, number of threads is defined by `multiprocessing.cpu_count()` (default: False)
  -s {wmean,mean,median,min,max,1pgeom}, --sumfunc {wmean,mean,median,min,max,1pgeom}
                        Summary function to calculate density for bin with. (default: wmean)
  -u UBIN, --ubin UBIN  Number of windows for upstream region (default: 50)
  -d DBIN, --dbin DBIN  Number of windows for downstream downstream (default: 50)
  -b BBIN, --bbin BBIN  Number of windows for body region (default: 100)
  -q QUANTILE, --quantile QUANTILE
                        Quantile of most varying genes to draw on clustermap (default: 0.75)
  -C CONFIDENCE, --confidence CONFIDENCE
                        Probability for confidence bands for line-plot. 0 if disabled (default: 0.95)
  -S SMOOTH, --smooth SMOOTH
                        Windows for SavGol function. (default: 10)
  -H VRESOLUTION        Vertical resolution for heat-map (default: 100)
  -V HRESOLUTION        Vertical resolution for heat-map (default: 100)
  --separate_strands    Do strands need to be processed separately (default: False)
  --export {pdf,svg,none}
                        Export format for plots (set none to disable) (default: pdf)
  --ticks TICKS TICKS TICKS TICKS TICKS
                        Names of ticks (5 labels with ; separator in " brackets) (default: None)

bsxplorer-category

bsxplorer-category --help
usage: BSXplorer-Categorise [-h] [-o NAME] [--dir DIR] [-m BLOCK_MB] [-t] [-s {wmean,mean,median,min,max,1pgeom}] [-u UBIN] [-d DBIN] [-b BBIN] [-q QUANTILE] [-C CONFIDENCE] [-S SMOOTH] [-H VRESOLUTION] [-V HRESOLUTION]
                            [--separate_strands] [--export {pdf,svg,none}] [--ticks TICKS TICKS TICKS TICKS TICKS] [--cytosine_p CYTOSINE_P] [--min_cov MIN_COV] [--region_p REGION_P] [--save_cat | --no-save_cat]
                            config

BM, UM categorisation tool

positional arguments:
  config                Path to config file

optional arguments:
  -h, --help            show this help message and exit
  -o NAME, --out NAME   Output filename (default: Metagene_Report_12-02-24_10-51-50)
  --dir DIR             Output and working dir (default: $CWD)
  -m BLOCK_MB, --block_mb BLOCK_MB
                        Block size for reading. (Block size ≠ amount of RAM used. Reader allocates approx. Block size * 20 memory for reading.) (default: 50)
  -t, --threads         Do multi-threaded or single-threaded reading. If multi-threaded option is used, number of threads is defined by `multiprocessing.cpu_count()` (default: False)
  -s {wmean,mean,median,min,max,1pgeom}, --sumfunc {wmean,mean,median,min,max,1pgeom}
                        Summary function to calculate density for bin with. (default: wmean)
  -u UBIN, --ubin UBIN  Number of windows for upstream region (default: 50)
  -d DBIN, --dbin DBIN  Number of windows for downstream downstream (default: 50)
  -b BBIN, --bbin BBIN  Number of windows for body region (default: 100)
  -q QUANTILE, --quantile QUANTILE
                        Quantile of most varying genes to draw on clustermap (default: 0.75)
  -C CONFIDENCE, --confidence CONFIDENCE
                        Probability for confidence bands for line-plot. 0 if disabled (default: 0.95)
  -S SMOOTH, --smooth SMOOTH
                        Windows for SavGol function. (default: 10)
  -H VRESOLUTION        Vertical resolution for heat-map (default: 100)
  -V HRESOLUTION        Vertical resolution for heat-map (default: 100)
  --separate_strands    Do strands need to be processed separately (default: False)
  --export {pdf,svg,none}
                        Export format for plots (set none to disable) (default: pdf)
  --ticks TICKS TICKS TICKS TICKS TICKS
                        Names of ticks (5 labels with ; separator in " brackets) (default: None)
  --cytosine_p CYTOSINE_P
                        P-value for binomial test to consider cytosine methylated (default: .05)
  --min_cov MIN_COV     Minimal coverage for cytosine to keep (default: 2)
  --region_p REGION_P   P-value for binomial test to consider region methylated (default: .05)
  --save_cat, --no-save_cat
                        Does categories need to be saved (default: True) (default: True)

bsxplorer-chr

bsxplorer-chr --help     
usage: BSXplorer-ChrLevels [-h] [-o NAME] [--dir DIR] [-m BLOCK_MB] [-t THREADS] [-w WINDOW] [-l MIN_LENGTH] [-C CONFIDENCE] [-S SMOOTH] [--export {pdf,svg,none}] [--separate_strands] config

Chromosome methylation levels visualisation tool

positional arguments:
  config                Path to config file

optional arguments:
  -h, --help            show this help message and exit
  -o NAME, --out NAME   Output filename (default: Metagene_Report_12-02-24_10-52-40)
  --dir DIR             Output and working dir (default: $CWD)
  -m BLOCK_MB, --block_mb BLOCK_MB
                        Block size for reading. (Block size ≠ amount of RAM used. Reader allocates approx. Block size * 20 memory for reading.) (default: 50)
  -t THREADS, --threads THREADS
                        Do multi-threaded or single-threaded reading. If multi-threaded option is used, number of threads is defined by `multiprocessing.cpu_count()` (default: True)
  -w WINDOW, --window WINDOW
                        Length of windows in bp (default: 1000000)
  -l MIN_LENGTH, --min_length MIN_LENGTH
                        Minimum length of chromosome to be analyzed (default: 1000000)
  -C CONFIDENCE, --confidence CONFIDENCE
                        Probability for confidence bands for line-plot. 0 if disabled (default: 0.95)
  -S SMOOTH, --smooth SMOOTH
                        Windows for SavGol function. (default: 10)
  --export {pdf,svg,none}
                        Export format for plots (set none to disable) (default: pdf)
  --separate_strands    Do strands need to be processed separately (default: False)