A robust, parallelized Python CLI for annotating three_prime_UTR
Project description
peaks2utr: a robust, parallelized Python CLI for annotating 3' UTR
Installation
Install latest release with:
pip install peaks2utr
Alternatively, to install from source:
git clone https://github.com/haessar/peaks2utr.git
cd peaks2utr
python3 -m build
python3 -m pip install dist/*.tar.gz
Dependencies
Installation instructions assume a Debian / Ubuntu system with root privileges. Follow the links for instructions for other systems.
Required
apt-get install bedtools
Optional
GenomeTools (for post-processing of output gff3)
apt-get install genometools
Quick start
Download demo reference annotations Tb927_01_v5.1.gff and bam file Tb927_01_v5.1.slice.bam and run
peaks2utr Tb927_01_v5.1.gff Tb927_01_v5.1.slice.bam
When complete, you should see a file Tb927_01_v5.1.new.gff
which contains original annotations as well as 3' UTRs with source "peaks2utr".
Project details
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Source Distribution
peaks2utr-0.4.tar.gz
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Built Distribution
peaks2utr-0.4-py3-none-any.whl
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