py-cortex-api

Python API for cortex.

Install

Latest release:

pip3 install py-cortex-api

Latest source:

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

Requirements

R is required by cortex at runtime.

sudo apt install r-base-core

Usage

Inputs:

• a reference genome in fasta[.gz]
• one or more reads file in fasta/q[.gz]

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

Output: A vcf with variants detected by cortex.

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

The third argument is where to place the output vcf.

Options

The following options can be passed to cortex.run:

• sample_name: sample name to appear in output vcf (default: 'sample').
• ploidy: 1 or 2, for haploid or diploid genotyping (default: 1)
• mem_height: if cortex.calls fails warning of too low memory, use a higher value (default: 22).
• tmp_directory: where to place intermediate output and log files (default: system-defined)
• cleanup: whether to remove intermediate output and log files upon successful completion. (Default: True)

Licence

MIT