getIntensities_wiki

Running method: getIntensities

All possible command line arguments for method getIntensities

Argument	Defaults	Description
--bpm	required by user	Full path to bead pool manifest file (.bpm); must be same one used to generate gtc
--gtcDir	required by user	Full path to location of directory/folder containing gtc files to process (files must end in .gtc) -- will not recursively go into sub-directories
--outDir	optional, default=current working directory	Full path to directory or folder to output results. If it path does not exist, program will attempt to create it
--logName	optional, default=gtcFuncs.log	Name of log file to output, will be created in directory --outDir
--modDir	optional, default=current working directory	Full path to module files .py from github; default is current working directory with modules folder appended
--prefix	optional, default=None	string prefix to name image files, will be created in directory --outDir.
--fileOutName	optional, default=controlProbeIntensityValues.txt	Name of final text file to output, will be created in directory --outDir
--recursive	optional, flag	if flag is specified, gtc files will be found recursively from the base --gtcDir, otherwise, only gtcs listed in --gtcDir will be used

The minimum command required to get sample information from files is the following:

python3 gtcFuncs.py getIntensities --bpm /path/to/manifest.bpm --gtcDir /path/to/gtcLocations/

This would create a tab-delimited text file called controlProbeIntensityValues.txt using all gtcs located in the argument following --gtcDir in the current working directory, along with a log file called gtcFuncs.log in the current working directory and an image for each control probe. For an example of the output, please click here.