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# A real-world example

## Python Code

The full code is available here.

## Running simulation studies with genes and GWAS data

### Background:

> Genome-wide association studies allow the underlying genetic factors behind common conditions like schizophrenia, obesity and heart disease to be identified.

> However, it is very import to make sure that the associations are statistically sound. This study uses 100 simulated data per gene / GWAS data to test the statistical significance.

### Aim:

> For each gene / GWAS data pair, we need to

> - run a simulation study 100 times against a reference set of (100) simulated data
> - calculate the mean probability for each gene

### Conceptual Flow chart:

> Our pipeline has just 2 steps:

> 1. Simulation. In pseudo code:

>        for n_file in NNN genes:
>             for m_file in MMM simulations:

>                 [n_file.gene,
>                  n_file.gwas,
>                  m_file.simulation] -> n_file.m_file.simulation_res

> 2. Summarise the simulations as a mean. In pseudo code:

>        for n_file in NNN genes:

>            n_file.*.simulation_res -> n_file.mean

### Challenges:

> The first step involves an N x M operation.

> These are unnecessary tricky to get right in `gmake` and like-minded build tools.

> In normal computer languages, this is just a pair of for loops:

>     for n in NNN:
>         for m in MMM:
>             do n x m

> The ruffus code is as simple.

### 1. Simulations per gene

> Notice the nested pair of for loops when generating the simulation parameters:

>     def generate_simulation_params ():

>         for sim_file in get_simulation_files():
>             for gene, gwas in get_gene_gwas_file_pairs():

>                 result_file = "%s.%s.simulation_res" % (gene, sim_file)
>                 yield [gene, gwas, sim_file], result_file

> This has been edited for clarity. The full function is available here.

> These parameters are passed to the python function calculating the simulations.

> We represent this with the following dummy function:

>     @follows(mkdir(output_dir))
>     @files(generate_simulation_params)
>     def gwas_simulation(input_files, result_file):
>         """
>         Dummy calculation of gene gwas vs simulation data
>         Normally runs in parallel on a computational cluster
>         """
>         (gene_file,
>         gwas_file,
>         simulation_data_file) = input_files

>         simulation_res_file = open(result_file, "w")

### 2. Mean simulated probability per gene

> Now all we have to do is gather all the simulation results, and caculate a mean probability per gene.

> Parameters for this “many -> 1” operation can be generated using a simple call to the glob module:

>     def generate_statistical_summary_params():
>         for gene, gwas in get_gene_gwas_file_pairs():
>             result_files     = glob.glob("%s.*.simulation_res" % (gene))
>             summary_file     = gene + ".mean"

>             yield result_files, summary_file

> The function for calculating means would resemble this:

>     @follows(gwas_simulation)
>     @files(generate_statistical_summary_params)
>     def statistical_summary (result_files, summary_file):
>         summary_file = open(summary_file, "w")

>         # ... more code to parse probabilities from results and calculate their mean

### Conclusions

What would be spaghetti in makefile format looks just like normal python code with ruffus.

### Navigation

- index
- modules |
- next |
- previous |
Ruffus v. 1.0.8
- Home |
- Contents |
- Cheat sheet |
- Full tutorial |
- FAQ |
- Future plans |
- Search »