Installation

The recommended installation is using the conda environment manager. You can find installation instructions for your operating system here.

First, checkout the the code from Github

bash$ git clone https://github.com/tyjo/coptr
bash$ cd coptr/

You can then create a new environment to run coPTR:

# creates an environment called coptr
$ conda env create -f coptr.yml

# you only need to create this once
# to activate the environment:
$ conda activate coptr
$ pip install .

To check if you can run CoPTR:

$ coptr

usage: coptr.py <command> [options]

command: index            create a bowtie2 index for a reference database
         map              map reads against a reference database
         merge            merge BAM files from reads mapped to multiple indexes
         extract          compute coverage maps from bam files
         estimate         estimate PTRs from coverage maps
         count            compute read counts for each genome after filtering

CoPTR (v1.0.0): Compute PTRs from complete reference genomes and assemblies.

positional arguments:
  command     Command to run.

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

Dependencies

Installation using conda iswill install all required dependencies. However, CoPTR’s dependencies are listed below if you wish to install them manually.

• bowtie2 (>=2.4.1): CoPTR assumes bowtie2 is install and accessible from your PATH variable

• python (>=3.7.8)

• matplotlib (>=3.3.2)

• numpy (=1.19.1)

• scipy (=1.5.2)

• pysam (=0.16.0.1)