galEupy

Python module for GAL. It does data processing.

Installation

For latest pip version

pip install galEupy

For latest development version

pip install git+https://github.com/computational-genomics-lab/galEupy.git

or

git clone https://github.com/computational-genomics-lab/galEupy.git
cd galEupy
pip install .

Usage

galEupy --help

Welcome to galEupy
usage: galEupy [-h] [-db DBCONFIG] [-path PATHCONFIG] [-org ORGCONFIG] [-upload {all,centraldogma,proteinannotation}] [-info [INFO]] [-org_info [ORG_INFO]]
               [-remove_org [REMOVE_ORG]] [-remove_db [REMOVE_DB]] [-v {none,debug,info,warning,error,d,e,i,w}] [-log LOG_FILE]

optional arguments:
  -h, --help            show this help message and exit
  -db DBCONFIG, --dbconfig DBCONFIG
                        Database configuration file name
  -path PATHCONFIG, --pathconfig PATHCONFIG
                        path configuration file name
  -org ORGCONFIG, --orgconfig ORGCONFIG
                        Organism configuration file name
  -upload {all,centraldogma,proteinannotation}, --upload {all,centraldogma,proteinannotation}
                        Upload data using different levels
  -info [INFO], --info [INFO]
                        Gives information of the table status
  -org_info [ORG_INFO], --org_info [ORG_INFO]
                        Gives information of an organism's upload status
  -remove_org [REMOVE_ORG], --remove_org [REMOVE_ORG]
                        Removes an organism details from the database
  -remove_db [REMOVE_DB], --remove_db [REMOVE_DB]
                        Removes the entire GAL related databases
  -v {none,debug,info,warning,error,d,e,i,w}, --verbose {none,debug,info,warning,error,d,e,i,w}
                        verbose level: debug, info (default), warning, error
  -log LOG_FILE, --log_file LOG_FILE
                        log file

Upload a Genome data

Usage to upload a genome

galEupy -db <db_configuration_file> -org <organism_configuration_file> -path <path_configuration_file> -v d -upload All

Both database and organism configuration files are required to upload the genome. Configuration files are in ini format.

Format for database configuration file

[dbconnection]
db_username : 
db_password : 
host : 
db_name : 
port:

Format for organism configuration file

The version denotes the different strains of the same species if they are available. So in the configuration file, the first strain to be uploaded has version: 1, the second strain has version: 2 and so on. If the user has different assemblies of the same strain, they can specify the following using "assembly_version:".

[OrganismDetails]
Organism:
version: 1
source_url:

[SequenceType]
SequenceType: chromosome
scaffold_prefix:

[filePath]
FASTA:
GFF:
eggnog: 

View GAL database log

Usage:

galEupy -v d -db <db_configuration_file> -info

Remove an organism from gal database

Usage

galEupy -v d -db <db_configuration_file> -org <organism_configuration_file> -remove_org

Here, it finds the organism details for the organism configuration file and then deletes the records related it.

Remove entire GAL related databases

Usage

galEupy -v d -db <db_configuration_file> -remove_db

Running uploader pipeline

A pipeline has been written in bash, called "bashpipeline", which is present in the directory "upload_pipeline". It also contains a python file called "id_replace.py", which is required for pre-processing eggnog files.

Usage

./bashpipeline

The pipeline will prompt the user to enter the location of the database configuration file, the file containing list of accession ids to consider as well as the path for the NCBI datasets along with the eggnog emapper files.