/py-cortex-api

Python API for cortex

Primary LanguagePython

py-cortex-api

Python API for cortex.

Install

pip3 install git+https://github.com/iqbal-lab-org/py-cortex-api

Requirements

R and python 2 are required.

sudo apt install r-base-core python2.7

Usage

Use a list to pass in reads files, even if there is only one file.

import cortex.calls as cortex
cortex.run("./reference.fasta",
             ["./reads.fastq"],
             "./output.vcf")

The third argument is where to place the output vcf.

Options

That can be passed to cortex.calls:

  • sample_name: sample name to appear in output vcf.
  • mem_height: if cortex.calls fails warning of too low memory, use higher than the default of 22.
  • tmp_directory: where to place intermediate output and log files
  • cleanup: whether to remove intermediate output and log files upon successful completion. (Default: True)

Licence

MIT