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