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Description:

badlon 0.1.3

Badlon
Installation
Bablon can be installed with pip:
pip install badlon

Now you can run tool from any directory as badlon.
Pipeline Usage
Modules
Badlon includes multiple modules to process data. They can be listed with help command:
$ badlon --help
usage: badlon [-h] {prepare,analysis,match} ...

Tool for block based analysis of bacterial populations. Choose one of available modules.

positional arguments:
{prepare,analysis,match}
prepare Prepare draft dataset for SibeliaZ.
analysis Analyze pan-genome and other block-based features based on synteny blocks.
match Performs matching of block and genes based on coordinates.

optional arguments:
-h, --help show this help message and exit

Here is recommended pipeline to process data with badlon:
Step 1: prepare data with PanACoTA pipeline
If you have genomes in some folder called some_folder (one file for genome), we suggest preparing data for badlon using PanACoTA pipeline.
To do so, you can use those commands:
1.1 Preparing data and tables with PanACoTA prepare module:
PanACoTA prepare --norefseq --min 0 --max 1 -o 1-prepare -d some_folder --cutn 125

--min 0 --max 1 are used to keep all genomes, parameter can be changed depending on task as well as all other parameters;
For check other parameters visit PanACoTA prepare documentation.

1.2 Annotating genomes with PanACoTA annotate module:
PanACoTA annotate --info 1-prepare/L* -r 2-annotate -n ESCO --threads 16

You can change label -n ESCO depending on your species (ESCO is for Escherichia coli);
For check parameters visit PanACoTA annotate documentation.

1.3 Calling orthology genes using PanACoTA pangenome module:
PanACoTA pangenome -l 2-annotate/LSTINFO-* -n ESCO -d 2-annotate/Proteins/ -o 3-pangenome

You can change -i which is minimum sequence identity to be considered in the same cluster (float between 0 and 1). Default is 0.8.
For check parameters visit PanACoTA pangenome documentation.

Step 2: Preparing data for alignment with badlon prepare module
Prepare module is used to prepare data for using SibeliaZ package keeping all necessary information: genome labels and chromosome numbers.
Parameters can be checked with help option:
$ badlon prepare --help
usage: badlon prepare [-h] --folder FOLDER [--contigs CONTIGS]
[--output OUTPUT]
[--annotate_subfolder ANNOTATE_SUBFOLDER]
[--min_len MIN_LEN]

optional arguments:
-h, --help show this help message and exit
--contigs CONTIGS, -c CONTIGS
Number of maximum contigs to take from every genome.
By default, keeps all.
--output OUTPUT, -o OUTPUT
Output file path.
--annotate_subfolder ANNOTATE_SUBFOLDER, -a ANNOTATE_SUBFOLDER
Subfolder of PanACoTA contains results of annotate
module. Used for finding LSTINFO file. Default is
'2-annotate'.
--min_len MIN_LEN, -l MIN_LEN
Minimum contig length, less then that value will be
filtered. Default is 1000.

Required arguments:
--folder FOLDER, -f FOLDER
Folder with PanACoTA output. Will be used to search
genome files based on LSTINFO file from annotate
module.

Example command:
badlon prepare -f 2-annotate -o for_sibeliaz.fna

Step 3: Obtaining blocks with SibeliaZ
3.1 Running SibeliaZ with recommended command based on badlon prepare output.
Example:
sibeliaz -k 15 -a 100 -n -t 32 -o sibeliaz_out for_sibeliaz.fna

Watch out -a it needs to be equal around number_of_genome * 20, badlon prepare calculates it automatically.

3.2 Obtaining blocks from alignment
Check recommended command from badlon prepare module output. Usually it's (blocks minimal size 3000):
cd sibeliaz_out
echo $'30 150\n100 500\n500 1500' > fine.txt
maf2synteny -s fine.txt -b 3000 blocks_coords.gff

Step 4: Calculating block based statistics and charts with badlon analysis module:
Parameters can be checked with help option:
$ badlon analysis --help
usage: badlon analysis [-h] --blocks_file BLOCKS_FILE --type {chr,contig}
[--output OUTPUT]

optional arguments:
-h, --help show this help message and exit
--output OUTPUT, -o OUTPUT
Path to output folder. Default: blockomics_output.

Required arguments:
--blocks_file BLOCKS_FILE, -b BLOCKS_FILE
Blocks resulted as output of original Sibelia or
maf2synteny tool. Usually it's
sibeliaz_out/3000/block_coords.txt file.
--type {chr,contig}, -t {chr,contig}
Type of genome assembly, either 'chr' or 'contig'

Example command:
cd ..
badlon analysis -b sibeliaz_out/3000/blocks_coords.txt

Step 5 (optional): Match block and genes annotation with badlon match module
Parameters can be checked with help option:
$ badlon match --help
usage: badlon match [-h] --blocks_file BLOCKS_FILE --annotated_folder
ANNOTATED_FOLDER --pangenome_file PANGENOME_FILE --type
{chr,contig} [--output OUTPUT]

optional arguments:
-h, --help show this help message and exit
--output OUTPUT, -o OUTPUT
Path to output folder. Default: blockomics_output.

Required arguments:
--blocks_file BLOCKS_FILE, -b BLOCKS_FILE
Blocks folder resulted as output of original Sibelia
or maf2synteny tool. Usually it's `sibeliaz_out/3000/`
folder.
--annotated_folder ANNOTATED_FOLDER, -a ANNOTATED_FOLDER
LSTINFO folder path, output of `annotate` step of
PanACoTA.
--pangenome_file PANGENOME_FILE, -pg PANGENOME_FILE
File .lst with orthologous genes, output of
`pangenome` step of PanACoTA.
--type {chr,contig}, -t {chr,contig}
Type of genome assembly, either 'chr' or 'contig'

Example command:
badlon match -b sibeliaz_out/3000/blocks_coords.txt -a 2-annotate/ -pg 3-pangenome/*.lst -t contig