Metadata-Version: 1.0
Name: regionanalysis
Version: 0.1
Summary: A utility to annotate genomic intervals.
Home-page: http://github.com/shenlab-sinai/region_analysis
Author: Ning-Yi SHAO
Author-email: shaoningyi@gmail.com
License: GPLv3
Description: ***************
        region_analysis
        ***************
        
        Dependency:
        ###########
        
        bedtools: https://code.google.com/p/bedtools/
        
        pybedtools: https://github.com/daler/pybedtools
        
        ::
        
            If easy_install or pip is available, then:
        
              easy_install pybedtools
        
              or:
        
              pip isntall pybedtools
        
        Usage: 
        ######
        
        region\_analysis.py [options]
        
        Options:
        ########
        
        -h, --help show this help message and exit
        
        -i INPUT\_FILE\_NAME, --input=INPUT\_FILE\_NAME
        
        ::
        
                                Input region file must assume the first 3 columns contain (chr, start, end)
        
        -d ANNO\_DB, --database=ANNO\_DB
        
        ::
        
                                Choose database: refseq(default) or ensembl
        
        -r, --rhead Whether the input file contains column header
        
        -g GENOME, --genome=GENOME
        
        ::
        
                                Choose genome: mm10(default)
        
        Output:
        #######
        
        	*-.annotated: the one-to-one output list, only the annotation entry whose TSS is nearest to the inquiry interval kept.
        
        	*-.full.annotated: all hit entries are kept.
        
        	*-.full.annotated.json: the json format output of -.full.annotated.
        
        Features:
        #########
        
        	*ProximalPromoter: +/- 250bp of TSS
        
        	*Promoter1k: +/- 1kbp of TSS
        
        	*Promoter3k: +/- 3kbp of TSS
        
        	*Genebody: Anywhere between a gene's promoter and up to 1kbp downstream of the TES.
        
        	*Genedeserts: Genomic regions that are depleted with genes and are at least 1Mbp long.
        
        	*Pericentromere: Between the boundary of a centromere and the closest gene minus 10kbp of that gene's regulatory region.
        
        	*Subtelomere: Similary defined as pericentromere.
        
        	*OtherIntergenic: Any region that does not belong to the above categories.
        
        Testing with examples:
        ######################
        
        	region\_analysis.py -i example/test\_without\_header.bed -g mm10 -d ensembl
        
        	region\_analysis.py -i example/test\_with\_header.bed -g mm10 -d ensembl -r
Platform: UNKNOWN
