About

Circular visualizer for complete genomes

Input: GenBank files (.gb)

Usage:

python runAllProcess.py <output directory> <input directory (GenBank files)>

Requirements

• BLAST+ (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
• Circos (http://circos.ca/)
• python 3 & modules
  • pandas, numpy, biopython, tqdm

PATH

You need to add the blast+/bin and the circos/bin to your PATH. Please check below.

echo $PATH
blastn -h
circos -h

Run

Run all processes

python runAllProcess.py <output directory> <input directory (GenBank files)>

Two required arguments are as follows:

1. path to the output directory
2. path to the directory containing GenBank files (.gb)

Run after the blastp processes

python runAfterBlastProcess.py <output directory> <input directory (GenBank files)>

Two required arguments are as follows:

1. path to the output directory
2. path to the directory containing GenBank files (.gb)

Run singularity blastp, qsub jobs (for NIG supercomputer system)

module load singularity
python runOnlyBlast.py <output directory> <input directory (GenBank files)> <bin_singularity directory>

Three required arguments are as follows:

1. path to the output directory
2. path to the directory containing GenBank files (.gb)
3. path to the bin_singularity directory

Please run runAfterBlastProcesses.py explained above after finished all qsub jobs.

Run visualization

python runVisualize.py  <output directory> <configuration file> <option; key word for output; default:"test"> <option; the minimum number of genes in each cluster; default: 1> <option; sorting column name; default: None>

Five arguments are as follows:

1. path to the output directory
2. path to the configuration file. Please see below.
3. optional: suffix for the output image file. Default is "test".
4. optional: the minimum number of genes in each cluster for visualization. Default is 1.
5. optional: the column name in the configuration file for sorting. Default is None.

Configuration file

This file will be outputed as "RingOrder_*_df.tsv" by runAllProcess.py and runAfterBlastProcess.py. Please see ./testResult/RingOrder_aligned_df.tsv. and ./testResult/changed_setting.tsv for examples.

AccNo	Genome_size	Strand	Angle	Deviation (Aligned)	Deviation (Original)	optional
NC_000915.1	1667867	0	0	53.311	47.061	...
NC_014256.1	1673997	1	342	53.07	177.67	...
...	...	...	...	...	...	...

You can edit the visualization result, such as the number of genomes and the ring order, by deleting / reordering rows in this file.

• AccNo: GenBank accession number
• Genome_size: the genome size (bp)
• Strand: choice of the strand for alignment. 0 = original, 1 = complement
• Angle: rotation in degree for alignment. (-20)–359
• Deviation (Aligned): The deviation to the consensus after alignment
• Deviation (Original): The deviation to the consensus before alignment
• optional: you can add the new column for sorting the ring order.

Utility

Create orthologous gene cluster table

python runCreateOrthologousTable.py <output directory> <input directory (GenBank files)>

Two required arguments are as follows:

1. path to the output directory
2. path to the directory containing GenBank files (.gb)

output files (clustering result)

• "OrthologousGeneTag.tsv": locus tag matrix
• "OrthologousGenePosition.tsv": gene start position matrix

Test run

Test data: 5 Helicobacter pylori genomes

all processes

It takes 10 minutes (BLASTP 8 min, other 2 min) on a standalone desktop server of 16GB memory.

cd
git clone git@github.com:tipputa/Circular-genome-visualizer.git
python ~/Circular-genome-visualizer/bin/runAllProcess.py ~/Circular-genome-visualizer/test/ ~/Circular-genome-visualizer/test/gb/

RunVisualize. Configuring the visualization.

In this example, "changed_setting.tsv" is a modified configuring file, where the first row was deleted from /test/data/RingOrder_aligned_df.tsv.

python ~/Circular-genome-visualizer/bin/runVisualize.py ~/Circular-genome-visualizer/test/ ~/Circular-genome-visualizer/test/changed_setting.tsv "rm1genome" 4

"rm1genome" is a suffix for the output file (e.g. circos_rm1genome.png). The genes conserved in >= 4 genomes are visualized.

Citation

• Tada I, Tanizawa Y, Arita M. Visualization of consensus genome structure without using a reference genome. BMC Genomics. 2017;18(Suppl 2):208. doi:10.1186/s12864-017-3499-7.