Galaxy Operations Help Information (Python Version)
Name:
galaxyOps.py - Operations on Genomic Intervals, which is written in Python
Usage:
galaxyOps.py bed_file_1 [[bed_file_2]|[-swcb...]]
Descriptions:
galaxyOps.py provides the same operation as C version galaxyOps.
Options:
-s, --subSeg: Print segments that DO NOT overlap with the 2nd bed file
-w, --subWhole: Print regions that DO NOT overlap with the 2nd bed file
-c, --complement: complement of the regions of a bed file
-b, --build=N: build of the input file ( only used for complement )
-i, --interSeg: Return only overlapping segments of 2 input bed file
-a, --interAll: Return whole regions from the 1st file, which overlap.
-m, --minSize=N: minimum size of overlapping
-o, --unionMerge: Merge any overlapping regions of 2 bed files
-l, --unionLists: Lists all the original regions of 2 bed files
-r, --restrict: Restrict region size by minSize and maxSize
-x, --maxSize=N: maximum size of the region, only for -restrict
-j, --joinLists: Join two regions from two input files side by side.
-d, --covDensity: Coverage density of the region of two queries
-p, --proximity: Find proximity regions between two queries
-U, --upstream=N: Number of bps in upstream
-D, --downstream=N: Number of bps in downstream
-W, --within: Used for proximity
-t, --cluster: Find clusters in one input file
-z, --clusterSize=N: Size of cluster
-N, --numRegion=N: Num of regions in a cluster
-S, --clusterSingle: Clustering return single region
-1, --chromCol=N: chrom column number of the 1st file (default = 0)
-2, --startCol=N: start column number of the 1st file (default = 1)
-3, --stopCol=N: stop column number of the 1st file (default = 2)
-4, --strandCol2=N: strand col num of 2nd file (proximity only, default=5)
-5, --chromCol2=N: chrom column number of the 2nd file (default = 0)
-6, --startCol2=N: start column number of the 2nd file (default = 1)
-7, --stopCol2=N: stop column number of the 2nd file (default = 2)
-C, --chrom=N: Restrict to one chromsome
Example:
galaxyOps.py knowGenes.bed exons.bed -s > introns.bed
Find subregions in file knowGenes.bed, that don't overlap with file exons.bed, and redirect the result to file introns.bed