sjcab-peak2anno-db 0.1.1

Gene-backed peak-to-annotation BED resources for SJ/CAB workflows.

sjcab_peak2anno_db

Gene-backed peak-to-annotation BED resources for SJ/CAB workflows.

The package bundles gene BED files to keep the distribution small. It can generate these derived annotations from each bundled gene version:

• tss: 1 bp TSS intervals, strand-aware
• tes: 1 bp TES intervals, strand-aware
• deduplong: longest isoform per gene name, using column 4 as gene name and column 5 as isoform length

The package also bundles blacklist BED files. During install, each blacklist is written under ~/.sjcab_peak2anno_db/blacklists as a dated *.bed.20230411 file, with the current *.bed name refreshed as a symlink. CpG island (CGI) BED files for hg38, hg19, mm10, mm9, and mm39 are also bundled and installed into ~/.sjcab_peak2anno_db/cgi.

Supported species:

• hg19
• hg38
• mm10
• mm9
• sacCer3

Install

From TestPyPI:

python -m pip install -i https://test.pypi.org/simple/ sjcab_peak2anno_db

From a local checkout:

python -m pip install .

Generate User Data

After package installation, generate all available versions under ~/.sjcab_peak2anno_db:

sjcab-peak2anno-db install

That command installs the packaged gene BEDs, blacklists, and CGI BEDs into the cache directory.

To use a different data directory, set SJCAB_PEAK2ANNO_DB_PATH:

export SJCAB_PEAK2ANNO_DB_PATH=/path/to/sjcab_peak2anno_db
sjcab-peak2anno-db install

You can also pass --data-dir for one command:

sjcab-peak2anno-db install --data-dir /path/to/sjcab_peak2anno_db

Generated files are written as:

{data_dir}/{species}/{annotation}/{version}.bed
{data_dir}/{species}/{annotation}/default.bed
{data_dir}/blacklists/{name}.bed.20230411
{data_dir}/blacklists/{name}.bed

default.bed points to the latest parsed version for that species and annotation.

Download UCSC CpG island BED files for hg38, hg19, mm10, mm9, and mm39:

sjcab-peak2anno-db download-cgi

CGI files are written as:

{data_dir}/cgi/{species}_cgi.bed

Python Usage

import sjcab_peak2anno_db as db

print(db.supported_species())
print(db.versions("hg38", "gene"))
print(db.default_version("hg19", "tss"))

db.install_data()
print(db.path("hg38", "tss"))

Generate one derived file manually:

import sjcab_peak2anno_db as db

db.write_tss("genes.bed", "genes.tss.bed")
db.write_tes("genes.bed", "genes.tes.bed")
db.write_deduplong("genes.bed", "genes.deduplong.bed")

Command Line

sjcab-peak2anno-db list
sjcab-peak2anno-db install
sjcab-peak2anno-db install-blacklists
sjcab-peak2anno-db download-cgi
sjcab-peak2anno-db update
sjcab-peak2anno-db path hg38 gene
sjcab-peak2anno-db path hg38 tss --install