To install dependencies and install ctDNAtool, it's recommended to first create a new clean Conda environment, and then run:
This will install the dependencies as well as ctDNAtool. ctDNAtool will be installed in edit mode.
The software has two entrypoints:ctDNAtool, which contains the core functionality, andctDNAflow which defines a set of workflows, with what we consider the most common use cases of the tool.To see which commands are available and how to use them, use the--help flag as shown below:
or
To run the test suite with nox, check for formatting and linting errors, run:
To run just the linter, run:
To debug an invocation of the ctDNAtool, use the -d flag after ctDNAtool, as shown below.
ctDNAflow is a tool for running workflows, based on the commands found in ctDNAtool.The workflows are compositions of multiple commands from ctDNAtool, and are designed with usability in mind.
Usage:
$ctDNAflow length-data-bed-bin<reference_genome_path><BAM_file_path>$ctDNAflow length-data-chr-bin<reference_genome_path><BAM_file_path>
The following is an example of an invocation of the command length-data-chr-bin. The command generates length data froma BAM file and bins it in chromosomes, then writes the output to a .tsv file.
$ ctDNAflow length-data-chr-bin hg19.2bit sample.bam -o length_data.tsv
In the example above, the output is directed to the length_data.tsv file.
Further documentation can be found by passing --help after ctDNAflow, or after aspecific command.
The output of the commands are written to either a .pickle or .tsv file. For the commands concerning only length data, the defaultaction is to write the output to a .tsv file. The output can be written to a .picke file by passing the -p flag.For all other commands, the output is written to .pickle.The output can be directed using the -o option. If this is not provided, the output will be written to a default filename.
