Metadata-Version: 2.1
Name: py-cortex-api
Version: 2.1.0
Summary: Python API for cortex.
Home-page: https://github.com/iqbal-lab-org/py-cortex-api
License: UNKNOWN
Description: # py-cortex-api
        Python API for [cortex](https://github.com/iqbal-lab/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
        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.
        
        
        ```python
        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
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
