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A utility to annotate genomic intervals.

Project description

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region_analysis
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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), and rat (rn4). New genomes will be added. Any question or suggestion is welcome!

Dependency:
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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:
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region\_analysis.py [options]

Options:
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-h, --help show this help message and exit

-i INPUT\_FILE\_NAME, --input=INPUT\_FILE\_NAME

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Input region file must assume the first 3 columns contain (chr, start, end)

-d ANNO\_DB, --database=ANNO\_DB

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Choose database: refseq(default) or ensembl

-r, --rhead Whether the input file contains column header

-g GENOME, --genome=GENOME

::

Choose genome: mm10(default), mm9, hg19, rn4

-v, --version

::

Version of Region_Analysis package
Output:
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*-.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:
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*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:
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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

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