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badlon-0.1.2
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مشاهده بیشترتوضیحات
A bioinf tool for analyzing pan-genome and other features based on synteny blocks
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | badlon-0.1.2 |
| نام | badlon |
| نسخه کتابخانه | 0.1.2 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Alexey Zabelkin |
| ایمیل نویسنده | a.zabelkin@itmo.ru |
| آدرس صفحه اصلی | https://github.com/oxygen311/badlon |
| آدرس اینترنتی | https://pypi.org/project/badlon/ |
| مجوز | - |
# Badlon
## Installation
Bablon can be installed with `pip`:
```bash
pip install badlon
```
Now you can run tool from any directory as `badlon`.
## Usage
### Modules
Badlon includes multiple modules to process data. They can be listed with help command:
```bash
$ 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
```
### Step 1: prepare data with [`PanACoTA` pipeline](https://github.com/gem-pasteur/PanACoTA)
If you have genomes in some folder called `some_folder` (one file for genome), we suggest preparing data using [`PanACoTA` pipeline](https://github.com/gem-pasteur/PanACoTA).
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`](https://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/usage.html#prepare-subcommand) 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 prepare`](https://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/usage.html#annotate-subcommand) 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 prepare`](https://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/usage.html#annotate-subcommand) documentation.
### Step 2: `prepare` module of `badlon`
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:
```bash
$ 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 2. Obtaining blocks with [SibeliaZ](https://github.com/medvedevgroup/SibeliaZ)
#### 2.1 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's needs to be equal around `number_of_genome * 20`, `badlon prepare` calculates it automatically.
#### 2.2 Obtaining blocks from alignment
Check recommended command from `badlon prepare` module output. Usually it's (blocks minimal size 3000):
```bash
cd sibeliaz_out
echo $'30 150\n100 500\n500 1500' > fine.txt
maf2synteny -s fine.txt -b 3000 blocks_coords.gff
```
### Step 3. Calculating block based statistics and charts with `badlon analysis` module:
Parameters can be checked with help option:
```bash
$ 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:
```bash
cd ..
badlon analysis -b sibeliaz_out/3000/blocks_coords.txt
```
### Step 4 (optional): Match block and genes annotation with `badlon match` module
Parameters can be checked with help option:
```bash
$ 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`
نیازمندی
| مقدار | نام |
|---|---|
| - | pandas |
| - | numpy |
| - | seaborn |
| - | biopython |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6, <4 | Python |
نحوه نصب
نصب پکیج whl badlon-0.1.2:
pip install badlon-0.1.2.whl
نصب پکیج tar.gz badlon-0.1.2:
pip install badlon-0.1.2.tar.gz