2.5. Extending RNFtools

This chapter describes how to develop an extension for a new read simulator.

2.5.1. Step 1: Wrapper of the simulator in RNFtools

All wrappers of read simulators are located in this directory: https://github.com/karel-brinda/rnftools/blob/master/rnftools/mishmash/. To create a new wrapper, copy some existing one and modify the code inside.

Method __init__ saves the parameters for a simulation. Some of them are mandatory (read length, FASTA file of the genome, etc.) and these are passed to __init__ of the mother abstract class for a simulator.

Method get_input returns list of input files for simulation and one of them is your program.

Method, create_fq simulates reads (by calling a shell command using rnftools.utils.shell) and converts the obtained files to RNF-FASTQ.

The previous step should be done using a dedicated static method (typically named recode_*_reads). All code for conversion should be located in this method so that it can be used externally without creating an instance of the class.

When all these functions are created/adjusted, the class should be imported in __init__.py. Get inspired by existing code, with a high probability only little changes will be needed.

2.5.2. Step 2: Support in the rnftools program

The last step is plugging your converting static function into rnftools console program, which is contained in this file: https://github.com/karel-brinda/rnftools/blob/master/rnftools/scripts.py. You will have to add a new subcommand (which will call the static function) and create a parser for it. Again, follow existing code.

2.5.3. Step 3: Tests

Add corresponding tests (see the test directory).