chicAggregateStatistic is a preprocessing tool for chicDifferentialTest. It takes two consecutive viewpoint files and one target file and creates one file containing all locations which should be tested for differential interactions. Either one target file for two consecutive viewpoint files or one target file for all viewpoints is accepted.

An example usage is:

$ chicAggregateStatistic –interactionFile viewpoint1.txt viewpoint2.txt –targetFile targets.txt –outFileNameSuffix aggregated.txt

which will create a single output file: viewpoint1_viewpoint2_aggregated.txt

A second mode is the batch processing mode. For this you need a file containing the names of the viewpoint files (generated by chicViewpoint via –writeFileNamesToFile), a folder which contains the files, a target list file containing the name of all target files and a folder which contains the target files (created by chicSignificantInteractions):

$ chicAggregateStatistic –interactionFile viewpoint_names.txt –targetFile target_names.txt –interactionFileFolder viewpointFilesFolder –targetFileFolder targetFolder –batchMode –threads 20 –outFileNameSuffix aggregated.bed

If the –targetFileFolder flag is not set in batch mode, it is assumed the –targetFile should be used for all viewpoints.

usage: chicAggregateStatistic --interactionFile INTERACTIONFILE
                              [INTERACTIONFILE ...]
                              [--targetFile TARGETFILE [TARGETFILE ...]]
                              [--outFileNameSuffix OUTFILENAMESUFFIX]
                              [--interactionFileFolder INTERACTIONFILEFOLDER]
                              [--targetFileFolder TARGETFILEFOLDER]
                              [--outputFolder OUTPUTFOLDER]
                              [--writeFileNamesToFile WRITEFILENAMESTOFILE]
                              [--batchMode] [--threads THREADS] [--help]

Required arguments

--interactionFile, -if

path to the interaction files which should be used for aggregation of the statistics.

--targetFile, -tf

path to the target files which contains the target regions to prepare data for differential analysis.

Optional arguments

--outFileNameSuffix, -suffix

File name suffix to save the result (Default: “_aggregate_target.txt”).

Default: “_aggregate_target.txt”

--interactionFileFolder, -iff

Folder where the interaction files are stored. Applies only for batch mode (Default: “.”).

Default: “.”

--targetFileFolder, -tff

Folder where the target files are stored. Applies only for batch mode.

--outputFolder, -o

Output folder containing the files (Default: “aggregatedFiles”).

Default: “aggregatedFiles”

--writeFileNamesToFile, -w

(Default: “aggregatedFilesBatch.txt”).

Default: “aggregatedFilesBatch.txt”

--batchMode, -bm

turns on batch mode. The files provided by –interactionFile and/or –targetFile contain a list of the files to be processed.

Default: False

--threads, -t

Number of threads (uses the python multiprocessing module)ist (Default: 4).

Default: 4


show program’s version number and exit