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region_analysis

Region_analysis is a package derived and extended from region_analysis.pl in diffReps package. It is a utility to annotate the genomic intervals like the peak list of ChIP-seq or other interval lists from the genomic research. Now it supports human (hg19), mouse (mm9, mm10), rat (rn4), chimpanzee (panTro4), rhesus macaque (rheMac2), and horse (equCab2). New genomes will be added. Any question or suggestion is welcome! If you want new genome to be added, please open an issue.

Dependency:

bedtools: https://code.google.com/p/bedtools/

pybedtools: https://github.com/daler/pybedtools

Installation

In terminal, just:

> python setup.py install

For debugging, just:

> python setup.py develop

After the installation, for testing:

> python setup.py test

(Not recommanded, because RA is under rapidly updating these days) If easy_install or pip is available, then:

> easy_install regionanalysis

or:

> pip isntall regionanalysis

Howtos

region_analysis.py

The utility to be used to annotate genomic intervals.

usage: region_analysis.py [-h] [-i INPUT] [-d DATABASE] [-r] [-g GENOME]
                          [-rv RAVER] [-v]

Annotate genomic intervals with RefSeq or Ensembl databases.

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input region file must assume the first 3 columns
                        contain (chr, start, end)
  -d DATABASE, --database DATABASE
                        Choose database: refseq(default) or ensembl
  -r, --rhead           Whether the input file contains column header
  -g GENOME, --genome GENOME
                        Choose genome: mm10(default)
  -rv RAVER, --RAver RAVER
                        Version of Region Analysis databases, default is the
                        newest
  -v, --version         Version of Region_Analysis package

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. In some cases,one interval may overlap with several features, e.g., at ProximalPromter in transcript A, at same time at Promoter3k feature in transcript B.
  • -.full.annotated.json: the json format output of -.full.annotated.

The annotations 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

region_analysis_db.py

Utility to manage the databases used by Region Analysis. The databases could be downloaded from databases folder of the repo. Now seven genomes are supported by Region Analysis, they are: equCab2, hg19, mm9, mm10, panTro4, rheMac2, and rn4.

usage: region_analysis_db.py [-h] {list,install,remove} ...

Manage annotation databases of region_analysis.

optional arguments:
  -h, --help            show this help message and exit

Subcommands:
  {list,install,remove}
                        additional help
    list                List genomes installed in database
    install             Install genome from tar.gz package file
    remove              Remove genome from database

To install new genome:

usage: region_analysis_db.py install [-h] [-y] pkg

positional arguments:
  pkg         Package file(.tar.gz) to install

optional arguments:
  -h, --help  show this help message and exit
  -y, --yes   Say yes to all prompted questions

To remove installed genome:

usage: region_analysis_db.py remove [-h] [-y] gn

positional arguments:
  gn          Name of genome to be removed(e.g. hg19)

optional arguments:
  -h, --help  show this help message and exit
  -y, --yes   Say yes to all prompted questions