BRIGaid

(SOS) BRIGaid generates xml files contaning the necessary data to aid in the execution of BRIG (Blast Ring Image Generator). This file will then be opened in BRIG and will fill all the necessary fields.

Usage (Commander)

% brigaid.py -q reference_sequence.fna -rfd path/to/reference/dir -od path/to/output/dir 
-of path/to/output/dir/output_file -oi path/to/output/BRIG/output_image -t Image_title 
-a annotation_file.gbk --genes genes_of_interest.txt --contig_order contig_order.tsv 
--blast_options "-evalue 0.001 -num_threads 6" --legend_pos upper-center 
--image_format png --height 3000 --width 3000 --java_memory 2000 --colormap viridis

Basic use (Human)

BRIGaid will generate an xml file with the necessary parameters to create an image using a reference file in .fasta format and the files contained on the reference directory and also indicates where the output of BRIG should go.

% brigaid.py -q reference_sequence.fna --ref_dir path/to/reference/dir 
--out_dir path/to/output/dir --out_xml path/to/output/dir/output_file 
--out_img path/to/output/BRIG/output_image --title Image_title 

Tweak BRIG options (Alien)

BRIGaid also allows the tweaking of some of BRIG's parameters such as:

• Arguments for Blast

% brigaid.py -q reference_sequence.fna --ref_dir path/to/reference/dir 
--out_dir path/to/output/dir --out_xml path/to/output/dir/output_file 
--out_img path/to/output/BRIG/output_image --title Image_title 
--blast_options "-evalue 0.001 -num_threads 6"

• Position of the legend of BRIG's output image.

% brigaid.py -q reference_sequence.fna --ref_dir path/to/reference/dir 
--out_dir path/to/output/dir --out_xml path/to/output/dir/output_file 
--out_img path/to/output/BRIG/output_image --title Image_title 
--legend_pos upper-center

• Format of BRIG's output image.

% brigaid.py -q reference_sequence.fna --ref_dir path/to/reference/dir 
--out_dir path/to/output/dir --out_xml path/to/output/dir/output_file 
--out_img path/to/output/BRIG/output_image --title Image_title 
--image_format png

• Height and width (in pixels) of BRIG's output image.

% brigaid.py -q reference_sequence.fna --ref_dir path/to/reference/dir 
--out_dir path/to/output/dir --out_xml path/to/output/dir/output_file 
--out_img path/to/output/BRIG/output_image --title Image_title 
--height 3000 --width 3000

• Amount of memory (in bytes) Java is allowed to use for BRIG.

% brigaid.py -q reference_sequence.fna --ref_dir path/to/reference/dir 
--out_dir path/to/output/dir --out_xml path/to/output/dir/output_file 
--out_img path/to/output/BRIG/output_image --title Image_title 
--java_memory 2000

• Colormap for the rings.

% brigaid.py -q reference_sequence.fna --ref_dir path/to/reference/dir 
--out_dir path/to/output/dir --out_xml path/to/output/dir/output_file 
--out_img path/to/output/BRIG/output_image --title Image_title 
--colormap viridis

Ring annotation (Time traveler)

BRIGaid accepts tab-delimited files or annotated Genbank files allowing the annotations of the rings.

Example of tab-delimited file:

#START	STOP	Label	Colour	Decoration
137680	139977	prot_1	black	clockwise-arrow
251394	253547	prot_2	black	clockwise-arrow

Command:

% brigaid.py -q reference_sequence.fna --ref_dir path/to/reference/dir 
--out_dir path/to/output/dir --out_xml path/to/output/dir/output_file 
--out_img path/to/output/BRIG/output_image --title Image_title 
--annotation annotations.gbk

It is also possible to provide a list of specific genes (one-per-line) to annotate the rings.

Example of a list of specific genes:

prot_1
prot_2
prot_3

Command:

% brigaid.py -q reference_sequence.fna --ref_dir path/to/reference/dir 
--out_dir path/to/output/dir --out_xml path/to/output/dir/output_file 
--out_img path/to/output/BRIG/output_image --title Image_title 
--annotation annotations.gbk --genes genes.txt

Ordering Contigs (Esper)

BRIGaid is able to order the contigs of the provided files by providing a simple tab-delimited file containing the preferred order of the contigs.

% brigaid.py -q reference_sequence.fna --ref_dir path/to/reference/dir 
--out_dir path/to/output/dir --out_xml path/to/output/dir/output_file 
--out_img path/to/output/BRIG/output_image --title Image_title 
--annotation annotations.gbk --contig_order contig_order.tsv

Example of possible tab-delimited file:

order   contig
1       Contig8
2       Contig10

Dependencies

• Biopython v1.74

Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423

• matplotlib v3.1.1

J. D. Hunter, "Matplotlib: A 2D Graphics Environment", Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95, 2007.