config module¶
It contains functions that handle configuration of gcMapExplorer. gcMapExplorer uses some default settings and options. This can be read and changed through these modules.
Configuration file structure¶
Configuration
├─────────── Dirs
│ └──────── WorkingDirectory
│
└─────────── Programs
├──────── bigWigInfo
└──────── bigWigToWig
Examples¶
import gcMapExplorer
gcMapExplorer.config.cleanScratch() # Clean default scratch directory
# Change scratch directory
gcMapExplorer.config.updateConfig('Dirs', 'WorkingDirectory', 'Path/to/new/scratch/directory')
# Set path to bigWigInfo program
gcMapExplorer.config.updateConfig('Programs', 'bigWigInfo', 'Path/to/bigWigInfo')
# Set path to bigWigToWig program
gcMapExplorer.config.updateConfig('Programs', 'bigWigToWig', 'Path/to/bigWigToWig')
# Print current configuration file content
gcMapExplorer.config.printConfig()
# Get configuration
config = gcMapExplorer.config.getConfig()
# Get scratch directory
print(config['Dirs']['WorkingDirectory'])
Summary¶
updateConfig (section, option, value) |
Update configuration file |
getConfig () |
To get the present configuration. |
printConfig () |
Print configuration file |
cleanScratch () |
Clean scratch directory. |
-
updateConfig
(section, option, value)¶ Update configuration file
Parameters:
-
getConfig
()¶ To get the present configuration.
Configuration file has the following organization.
Configuration ├─────────── Dirs │ └──────── WorkingDirectory │ └─────────── Programs ├──────── bigWigInfo └──────── bigWigToWig
In case no configuration file is found, a new file is generated and default value is assigned to each option.
Returns: config – Dictionary of Dictionaries with option name and value pair. For example, config[‘Dirs’][‘WorkingDirectory’] contains path to scratch directory. Similarly, config[‘Programs’][‘bigWigInfo’] contains path to bigWigInfo program. Return type: dict
-
printConfig
()¶ Print configuration file
It can be used to print the configuration file. It shows the current configuration of gcMapExplorer.
-
cleanScratch
()¶ Clean scratch directory.
It checks whether any other gcMapExplorer process is running. In case, when only one process (i.e. current) is running, all files with “gcx” prefix will be deleted from default scratch directory.