A CLI to create and annotate synteny plots for microbial genomes or plasmids. It uses GenBank files as input and creates alignment on the fly. It provides additional tools to edit the GenBank files to customize the synteny plot.
MUMmer and/or MMSeqs should be installed to run the aligner.
Install from PyPI
pip install PySyntenyViz
Install from source:
git clone https://github.com/acarafat/PySyntenyViz/
cd PySyntenyViz
pip install .
Alternatively to build and install from source using pip wheel:
pip install wheel
git clone https://github.com/acarafat/PySyntenyViz/
cd PySyntenyViz
python3 setup.py sdist bdist_wheel
pip install dist/bioinfutils-0.1.0-py3-none-any.whl --force-reinstall
synviz <command> [<args>]
Available commands: synteny, revcomp, reorder, change_origin
synteny: Generate synten plotchange_origin: Change origin of a GenBank filerevcomp: Reverse-complement particular contig or whole GenBank file sequencereorder: Reorder contigs of GenBakn file
Use -h or --h flag to get details of the command, i.e.: synviz <command> --help
There are two options for annotating the synteny plot. One option is by providing GenBank features, which will annotate the particular feature of interest based on its presence in the GenBank file. Another option is to provide exact coordinates, so that those coordinates will be annotated specifically.
Input file strainlist.txt:
/path/to/Strain_1.gbk
/path/to/Strain_2.gbk
/path/to/Strain_3.gbk
Coordinate file for annotation using --coordinate flag: coordinates.tsv
| gbk | locus | label | start | end | color | strand | plotstyle |
|---|---|---|---|---|---|---|---|
| Strain_1 | Contig_1 | nod | 5413 | 14992 | blue | 1 | box |
| Strain_1 | Contig_1 | nif/fix | 19407 | 42752 | magenta | 1 | box |
| Strain_1 | Contig_1 | nif/fix | 175637 | 187210 | magenta | 1 | box |
| Strain_1 | Contig_1 | T4SS | 357052 | 370816 | brown | 1 | box |
| Strain_1 | Contig_1 | bio | 377557 | 381609 | black | 1 | box |
| Strain_1 | Contig_1 | pan | 386274 | 387991 | black | 1 | box |
| Strain_1 | Contig_1 | nod | 391054 | 393012 | blue | 1 | box |
| Strain_1 | Contig_1 | nif/fix | 421473 | 429473 | magenta | 1 | box |
| Strain_1 | Contig_1 | T4SS | 557560 | 569180 | brown | 1 | box |
| Strain_2 | Contig_1 | nod | 3972 | 9259 | blue | 1 | box |
| Strain_2 | Contig_1 | nif/fix | 30871 | 44544 | magenta | 1 | box |
| Strain_2 | Contig_1 | nif/fix | 68132 | 84403 | magenta | 1 | box |
| Strain_2 | Contig_1 | bio | 297983 | 302023 | black | 1 | box |
| Strain_2 | Contig_1 | pan | 306814 | 308405 | black | 1 | box |
| Strain_2 | Contig_1 | nif/fix | 330400 | 338787 | magenta | 1 | box |
| Strain_2 | Contig_1 | T4SS | 392045 | 403669 | brown | 1 | box |
| Strain_3 | Contig_1 | nif/fix | 479987 | 488559 | magenta | 1 | box |
| Strain_3 | Contig_1 | T4SS | 467546 | 479162 | brown | 1 | box |
| Strain_3 | Contig_1 | T4SS | 429923 | 451808 | brown | 1 | box |
| Strain_3 | Contig_1 | nod | 369759 | 373679 | blue | 1 | box |
| Strain_3 | Contig_1 | nod | 357170 | 357766 | blue | 1 | box |
| Strain_3 | Contig_1 | nif/fix | 157877 | 164992 | magenta | 1 | box |
| Strain_3 | Contig_1 | nif/fix | 108463 | 122788 | magenta | 1 | box |
| Strain_3 | Contig_1 | bio | 78637 | 84154 | black | 1 | box |
| Strain_3 | Contig_1 | nod | 74067 | 77670 | blue | 1 | box |
Command for synteny plot:
synviz synteny --input_list strainlist.txt --output synteny_output.pdf --alignment mmseqs --coordinate coordinates.tsv
If you want to use feature types for generic annotation, use the --annotate flag and provide annotation.tsv file instead:
| feature_type | qualifier | value | face_color | label |
|---|---|---|---|---|
| CDS | product | bio | black | bio |
| gene | gene | nif | magenta | nif |
| gene | gene | nod | magenta | nod |
| gene | gene | fix | magenta | fix |
| mobile_element | mobile_element_type | T4SS | brown | ICE |
Command:
synviz synteny --input_list strainlist.txt --output synteny_output.pdf --alignment mmseqs --annotate annotate.tsv
Read GenBank files as input from directory, plot Agrobacterium synteny with MMSeqs2 alignment and annotate by GenBank feature:
synviz synteny --input_dir agrobacterium --output agro_original.png --annotate annotate_synteny.tsv --alignment mmseqs
Use MUMmer alignment instead:
synviz synteny --input_dir agrobacterium --output agro_original.mummer.png --annotate annotate_synteny.tsv
Reverse-complement a contig and plot synteny, take input from a list:
synviz revcomp -i agrobacterium/47_2_polished_final_renamed.gbk -o agrobacterium/47_2_polished_final_renamed.rc.gbk -c chromosome
synviz synteny --input_list agrolist.txt --output agro_rc.mmseqs.png --alignment mmseqs --annotate annotate_synteny.tsv
Reorder contigs by custom-order and plot synteny:
grep "LOCUS" agrobacterium/47_2_polished_final_renamed.rc.gbk
synviz reorder --input agrobacterium/47_2_polished_final_renamed.rc.gbk --output agrobacterium/47_2_polished_final_renamed.rc.order.gbk --order chromosome chromid pTi plasmid1 plasmid2
grep "LOCUS" agrobacterium/47_2_polished_final_renamed.rc.order.gbk
Reorder contigs by size and plot synteny:
grep "LOCUS" agrobacterium/47_2_polished_final_renamed.rc.gbk
synviz reorder --input agrobacterium/47_2_polished_final_renamed.rc.gbk --output agrobacterium/47_2_polished_final_renamed.rc.order.gbk --by_size
grep "LOCUS" agrobacterium/47_2_polished_final_renamed.rc.order.gbk
Change contig origin in GenBank file and plot synteny:
synviz change_origin -i agrobacterium/47_2_polished_final_renamed.rc.order.gbk -o agrobacterium/47_2_polished_final_renamed.rc.order.origin.gbk --origin 346694 --contig chromosome_rc
synviz synteny --input_list agrolist.txt --output agro_rc.mmseqs.png --alignment mmseqs --annotate annotate_synteny.tsv
Annotate synteny with specific feature coordinates:
synviz synteny --input_list bradylist.txt --output brady_original.mmseqs.png --alignment mmseqs --coordinate coordinates.tsv