SWMM — SeqWord Motif Mapper

SWMM (SeqWord Motif Mapper) is a Python program for visualizing and statistically evaluating the distribution of epigenetically modified nucleotides and motifs in bacterial genomes and metagenomic contigs.

SWMM provides two main workflows:

sort-contigs — sorts previously binned metagenomic contigs according to their methylation-motif patterns.
methylation-pattern — visualizes genome methylation patterns and evaluates the distribution of epigenetically modified bases.

General usage

Display the main help message:

python3 swmm.py --help

usage: swmm.py [-h] [-v]

Option	Description
`-h`, `--help`	Show the help message and exit.
`-v`, `--version`	Show the program version and exit.

Sort contigs

The sort-contigs command sorts binned contigs based on patterns of methylated motifs.

Help

python3 swmm.py sort-contigs --help

Usage

usage: sort_contigs.py [-h]
                       [-i INPUT_FOLDER]
                       [-o OUTPUT_FOLDER]
                       [-p PROJECT_FOLDER]
                       [-g GFF_FILE]
                       [-m MOTIFS]
                       [--output_graph_format {SVG,HTML,PDF,EPS,JPG,JPEG,TIF,TIFF,PNG,BMP}]
                       [-u {keep,split}]
                       [--filter_chimeric_contigs FILTER_CHIMERIC_CONTIGS]
                       [-c {Y,y,N,n}]
                       [--dpi DPI]
                       [--mqs MQS]
                       [-l SLIDING_WINDOW_LENGTH]
                       [-w SLIDING_WINDOW_STEP]
                       [--file_name_separator FILE_NAME_SEPARATOR]
                       [-s {Y,N,y,n}]

Arguments

Option	Description	Default
`-h`, `--help`	Show the help message and exit.	—
`-i INPUT_FOLDER`, `--input_folder INPUT_FOLDER`	Input folder.	`input`
`-o OUTPUT_FOLDER`, `--output_folder OUTPUT_FOLDER`	Output folder.	`output`
`-p PROJECT_FOLDER`, `--project_folder PROJECT_FOLDER`	Project folder.	Current directory
`-g GFF_FILE`, `--gff_file GFF_FILE`	GFF file containing epigenetic predictions. If omitted, the program searches for bin-specific GFF files.	Empty
`-m MOTIFS`, `--motifs MOTIFS`	Semicolon-separated motif definitions, for example `GATC,2,-2; CCWGG,2,-2`.	—
`--output_graph_format FORMAT`	Output format: `SVG`, `HTML`, `PDF`, `EPS`, `JPG`, `JPEG`, `TIF`, `TIFF`, `PNG`, or `BMP`.	`SVG`
`-u {keep,split}`, `--unresolved_contigs {keep,split}`	Keep or split unresolved contigs with statistically insignificant methylation patterns.	`keep`
`--filter_chimeric_contigs VALUE`	Filter contigs with a non-random distribution of modified sites. Accepts `Yes`, `No`, or a p-value satisfying `0 < p <= 0.05`.	`No`
`-c {Y,y,N,n}`, `--circular_graph {Y,y,N,n}`	Produce a circular graph.	`Y`
`--dpi DPI`	Output image resolution in dots per inch.	`600`
`--mqs MQS`	Minimum methylation quality score.	`20`
`-l LENGTH`, `--sliding_window_length LENGTH`	Sliding-window length.	`2000`
`-w STEP`, `--sliding_window_step STEP`	Sliding-window step.	`500`
`--file_name_separator SEPARATOR`	Separator used to select the basename as the first part of a filename.	Empty
`-s {Y,N,y,n}`, `--save_graphs {Y,N,y,n}`	Save generated graphs.	`Y`

Methylation pattern

The methylation-pattern command processes GFF files generated by ipdSummary, produces graphical representations, and performs statistical analysis of the distribution of epigenetically modified bases.

Help

python3 swmm.py methylation-pattern --help

General usage

python run.py [arguments]
python run.py -h
python run.py --help
python run.py -v
python run.py --version

Example

python program.py \
    -i input.gff \
    -g genome.gbk \
    -d example \
    -mm Y \
    -w GATC,2,-2 \
    -p 100 \
    -sp Y

This example:

Reads input.gff and genome.gbk from ./input/example.
Writes graphical and text output to ./output/example.
Searches for the motif GATC,2,-2.
Treats the second nucleotide from the left on the direct strand and the second nucleotide from the right on the reverse-complement strand as modified positions.
Sets the promoter length to 100 bp.
Enables circular-map visualization and motif-distribution statistics.

General settings

Option	Description	Default
`-d FOLDER`, `--project_directory FOLDER`	Project subfolder.	Empty
`-i FILE`, `--input_GFF FILE`	Input GFF filename. Required.	Empty
`-g FILE`, `--input_GBK FILE`	Input GenBank filename. Required.	Empty
`-m FILE`, `--filter_file FILE`	File defining regions to filter.	Empty
`-ft NAME`, `--generic_file_name NAME`	Generic output filename.	Empty
`-ogf FORMAT`, `--output_graph_format FORMAT`	Output format: `SVG`, `HTML`, `PDF`, `EPS`, `JPG`, `JPEG`, `TIF`, `TIFF`, `PNG`, or `BMP`.	`HTML`
`-dpi DPI`, `--dpi DPI`	Raster-image resolution from 100 to 1200 dpi.	`300`
`-p LENGTH`, `--promoter_length LENGTH`	Promoter-region length.	`75`
`-r NUMBER`, `--maximum_sites NUMBER`	Maximum number of sites to verify. Use `0` to skip checking.	`10000`
`-n NUMBER`, `--blast_context_mismatch NUMBER`	Allowed number of context mismatches.	`2`
`-z Yes/No`, `--blast_motif_mismatch Yes/No`	Allow motif mismatches.	`Yes`
`-u FOLDER`, `--input_folder FOLDER`	Input folder.	`input`
`-o FOLDER`, `--output_folder FOLDER`	Output folder.	`output`
`-x FOLDER`	Executable folder.	`./lib/bin`
`-tmp FOLDER`	Temporary folder.	`./lib/bin/tmp`

Circular-map settings

Option	Description	Default
`-mm Y/N`, `--circular_map Y/N`	Generate a circular plot.	`Y`
`-w MOTIF`, `--cmap_motif MOTIF`	Motif definition, for example `GATC,2,-2`.	—
`-s MODE`, `--sites_or_motifs MODE`	Search for sites or motifs. Accepted values include `sites`, `motifs`, `S`, and `M`.	`sites`
`-f M/U`, `--modified_or_unmodified M/U`	Display modified or unmodified motifs.	`M`
`-wl LENGTH`, `--window_length LENGTH`	Sliding-window length.	`8000`
`-ws STEP`, `--window_step STEP`	Sliding-window step.	`2000`
`-c SCORE`, `--cmap_score_cutoff SCORE`	Circular-plot score cutoff.	`21`
`-cmt TITLE`, `--cmap_graph_title TITLE`	Circular-map graph title.	Empty

Dot-plot settings

Option	Description	Default
`-dp Y/N`, `--dotplot Y/N`	Generate a dot plot.	`N`
`-dpn BASES`, `--nucleotides BASES`	Nucleotides to display: `A`, `C`, `G`, `T`, or an empty value.	`A,C`
`-dpm TYPES`, `--methylation_types TYPES`	Methylation types to display, such as `m6A` or `m4C`.	Empty
`-dpf MOTIFS`, `--dotplot_motifs MOTIFS`	Motifs to include or exclude, for example `GATC,2,-2; -CRGKGATC,1,6,-2`.	—
`-dpc SCORE`, `--dotplot_score_cutoff SCORE`	Dot-plot score cutoff.	`21`
`-dpw VALUE`, `--maximum_coverage VALUE`	Maximum coverage on the x-axis. Use `0` for automatic scaling.	`0`
`-dps VALUE`, `--maximum_score VALUE`	Maximum score on the y-axis. Use `0` for automatic scaling.	`0`
`-dpt TITLE`, `--dp_graph_title TITLE`	Dot-plot graph title.	Empty

Statistics settings

Option	Description	Default
`-sp Y/N`, `--statplot Y/N`	Generate a statistics panel.	`Y`
`-tsk TASKS`, `--tasks TASKS`	Statistical tasks, such as `gc`, `gcs`, and `mge`.	`gc,gcs`
`-std MODE`, `--strand MODE`	Exclude the `leading` or `lagging` strand, or use `off` to disable strand exclusion.	`off`
`-spt TITLE`, `--sp_graph_title TITLE`	Statistical-panel graph title.	Empty

Contact

For further information, refer to the project documentation or contact:

Oleg Reva
University of Pretoria
Email: oleg.reva@up.ac.za Library / README.md

SWMM — SeqWord Motif Mapper

SWMM (SeqWord Motif Mapper) is a Python program for visualizing and statistically evaluating the distribution of epigenetically modified nucleotides and motifs in bacterial genomes and metagenomic contigs.

SWMM provides two main workflows:

sort-contigs — sorts previously binned metagenomic contigs according to their methylation-motif patterns.
methylation-pattern — visualizes genome methylation patterns and evaluates the distribution of epigenetically modified bases.

General usage

Display the main help message:

python3 swmm.py --help

usage: swmm.py [-h] [-v]

Option	Description
`-h`, `--help`	Show the help message and exit.
`-v`, `--version`	Show the program version and exit.

Sort contigs

The sort-contigs command sorts binned contigs based on patterns of methylated motifs.

Help

python3 swmm.py sort-contigs --help

Usage

usage: sort_contigs.py [-h]
                       [-i INPUT_FOLDER]
                       [-o OUTPUT_FOLDER]
                       [-p PROJECT_FOLDER]
                       [-g GFF_FILE]
                       [-m MOTIFS]
                       [--output_graph_format {SVG,HTML,PDF,EPS,JPG,JPEG,TIF,TIFF,PNG,BMP}]
                       [-u {keep,split}]
                       [--filter_chimeric_contigs FILTER_CHIMERIC_CONTIGS]
                       [-c {Y,y,N,n}]
                       [--dpi DPI]
                       [--mqs MQS]
                       [-l SLIDING_WINDOW_LENGTH]
                       [-w SLIDING_WINDOW_STEP]
                       [--file_name_separator FILE_NAME_SEPARATOR]
                       [-s {Y,N,y,n}]

Arguments

Option	Description	Default
`-h`, `--help`	Show the help message and exit.	—
`-i INPUT_FOLDER`, `--input_folder INPUT_FOLDER`	Input folder.	`input`
`-o OUTPUT_FOLDER`, `--output_folder OUTPUT_FOLDER`	Output folder.	`output`
`-p PROJECT_FOLDER`, `--project_folder PROJECT_FOLDER`	Project folder.	Current directory
`-g GFF_FILE`, `--gff_file GFF_FILE`	GFF file containing epigenetic predictions. If omitted, the program searches for bin-specific GFF files.	Empty
`-m MOTIFS`, `--motifs MOTIFS`	Semicolon-separated motif definitions, for example `GATC,2,-2; CCWGG,2,-2`.	—
`--output_graph_format FORMAT`	Output format: `SVG`, `HTML`, `PDF`, `EPS`, `JPG`, `JPEG`, `TIF`, `TIFF`, `PNG`, or `BMP`.	`SVG`
`-u {keep,split}`, `--unresolved_contigs {keep,split}`	Keep or split unresolved contigs with statistically insignificant methylation patterns.	`keep`
`--filter_chimeric_contigs VALUE`	Filter contigs with a non-random distribution of modified sites. Accepts `Yes`, `No`, or a p-value satisfying `0 < p <= 0.05`.	`No`
`-c {Y,y,N,n}`, `--circular_graph {Y,y,N,n}`	Produce a circular graph.	`Y`
`--dpi DPI`	Output image resolution in dots per inch.	`600`
`--mqs MQS`	Minimum methylation quality score.	`20`
`-l LENGTH`, `--sliding_window_length LENGTH`	Sliding-window length.	`2000`
`-w STEP`, `--sliding_window_step STEP`	Sliding-window step.	`500`
`--file_name_separator SEPARATOR`	Separator used to select the basename as the first part of a filename.	Empty
`-s {Y,N,y,n}`, `--save_graphs {Y,N,y,n}`	Save generated graphs.	`Y`

Methylation pattern

The methylation-pattern command processes GFF files generated by ipdSummary, produces graphical representations, and performs statistical analysis of the distribution of epigenetically modified bases.

Help

python3 swmm.py methylation-pattern --help

General usage

python run.py [arguments]
python run.py -h
python run.py --help
python run.py -v
python run.py --version

Example

python program.py \
    -i input.gff \
    -g genome.gbk \
    -d example \
    -mm Y \
    -w GATC,2,-2 \
    -p 100 \
    -sp Y

This example:

Reads input.gff and genome.gbk from ./input/example.
Writes graphical and text output to ./output/example.
Searches for the motif GATC,2,-2.
Treats the second nucleotide from the left on the direct strand and the second nucleotide from the right on the reverse-complement strand as modified positions.
Sets the promoter length to 100 bp.
Enables circular-map visualization and motif-distribution statistics.

General settings

Option	Description	Default
`-d FOLDER`, `--project_directory FOLDER`	Project subfolder.	Empty
`-i FILE`, `--input_GFF FILE`	Input GFF filename. Required.	Empty
`-g FILE`, `--input_GBK FILE`	Input GenBank filename. Required.	Empty
`-m FILE`, `--filter_file FILE`	File defining regions to filter.	Empty
`-ft NAME`, `--generic_file_name NAME`	Generic output filename.	Empty
`-ogf FORMAT`, `--output_graph_format FORMAT`	Output format: `SVG`, `HTML`, `PDF`, `EPS`, `JPG`, `JPEG`, `TIF`, `TIFF`, `PNG`, or `BMP`.	`HTML`
`-dpi DPI`, `--dpi DPI`	Raster-image resolution from 100 to 1200 dpi.	`300`
`-p LENGTH`, `--promoter_length LENGTH`	Promoter-region length.	`75`
`-r NUMBER`, `--maximum_sites NUMBER`	Maximum number of sites to verify. Use `0` to skip checking.	`10000`
`-n NUMBER`, `--blast_context_mismatch NUMBER`	Allowed number of context mismatches.	`2`
`-z Yes/No`, `--blast_motif_mismatch Yes/No`	Allow motif mismatches.	`Yes`
`-u FOLDER`, `--input_folder FOLDER`	Input folder.	`input`
`-o FOLDER`, `--output_folder FOLDER`	Output folder.	`output`
`-x FOLDER`	Executable folder.	`./lib/bin`
`-tmp FOLDER`	Temporary folder.	`./lib/bin/tmp`

Circular-map settings

Option	Description	Default
`-mm Y/N`, `--circular_map Y/N`	Generate a circular plot.	`Y`
`-w MOTIF`, `--cmap_motif MOTIF`	Motif definition, for example `GATC,2,-2`.	—
`-s MODE`, `--sites_or_motifs MODE`	Search for sites or motifs. Accepted values include `sites`, `motifs`, `S`, and `M`.	`sites`
`-f M/U`, `--modified_or_unmodified M/U`	Display modified or unmodified motifs.	`M`
`-wl LENGTH`, `--window_length LENGTH`	Sliding-window length.	`8000`
`-ws STEP`, `--window_step STEP`	Sliding-window step.	`2000`
`-c SCORE`, `--cmap_score_cutoff SCORE`	Circular-plot score cutoff.	`21`
`-cmt TITLE`, `--cmap_graph_title TITLE`	Circular-map graph title.	Empty

Dot-plot settings

Option	Description	Default
`-dp Y/N`, `--dotplot Y/N`	Generate a dot plot.	`N`
`-dpn BASES`, `--nucleotides BASES`	Nucleotides to display: `A`, `C`, `G`, `T`, or an empty value.	`A,C`
`-dpm TYPES`, `--methylation_types TYPES`	Methylation types to display, such as `m6A` or `m4C`.	Empty
`-dpf MOTIFS`, `--dotplot_motifs MOTIFS`	Motifs to include or exclude, for example `GATC,2,-2; -CRGKGATC,1,6,-2`.	—
`-dpc SCORE`, `--dotplot_score_cutoff SCORE`	Dot-plot score cutoff.	`21`
`-dpw VALUE`, `--maximum_coverage VALUE`	Maximum coverage on the x-axis. Use `0` for automatic scaling.	`0`
`-dps VALUE`, `--maximum_score VALUE`	Maximum score on the y-axis. Use `0` for automatic scaling.	`0`
`-dpt TITLE`, `--dp_graph_title TITLE`	Dot-plot graph title.	Empty

Statistics settings

Option	Description	Default
`-sp Y/N`, `--statplot Y/N`	Generate a statistics panel.	`Y`
`-tsk TASKS`, `--tasks TASKS`	Statistical tasks, such as `gc`, `gcs`, and `mge`.	`gc,gcs`
`-std MODE`, `--strand MODE`	Exclude the `leading` or `lagging` strand, or use `off` to disable strand exclusion.	`off`
`-spt TITLE`, `--sp_graph_title TITLE`	Statistical-panel graph title.	Empty

Contact

For further information, refer to the project documentation or contact:

Oleg Reva
University of Pretoria
Email: oleg.reva@up.ac.za

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SWMM — SeqWord Motif Mapper

Contents

General usage

Sort contigs

Help

Usage

Arguments

Methylation pattern

Help

General usage

Example

General settings

Circular-map settings

Dot-plot settings

Statistics settings

Contact

SWMM — SeqWord Motif Mapper

Contents

General usage

Sort contigs

Help

Usage

Arguments

Methylation pattern

Help

General usage

Example

General settings

Circular-map settings

Dot-plot settings

Statistics settings

Contact

About

Releases

Packages

Contributors

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Name		Name	Last commit message	Last commit date
input		input
lib		lib
output		output
supplementary		supplementary
LICENSE		LICENSE
README(1).md		README(1).md
README.md		README.md
swmm.py		swmm.py

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SWMM — SeqWord Motif Mapper

Contents

General usage

Sort contigs

Help

Usage

Arguments

Methylation pattern

Help

General usage

Example

General settings

Circular-map settings

Dot-plot settings

Statistics settings

Contact

SWMM — SeqWord Motif Mapper

Contents

General usage

Sort contigs

Help

Usage

Arguments

Methylation pattern

Help

General usage

Example

General settings

Circular-map settings

Dot-plot settings

Statistics settings

Contact

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