Get Cluster PF % and Cluster Density from Interop module using python

Question

[kspata]

Greetings,

I am using inter op module in python to obtain %Q30, Cluster Density (K/mm2), and Cluster PF (%). I am implementing python interop module to obtain these files from the run folders.

I have following code to obtain Q30, where run folder is MiSeq run folder. I wish to automate this script as I have multiple folders.

run_metrics = py_interop_run_metrics.run_metrics()
        valid_to_load = py_interop_run.uchar_vector(py_interop_run.MetricCount, 0)
        py_interop_run_metrics.list_summary_metrics_to_load(valid_to_load)
        run_folder = run_metrics.read(run_folder, valid_to_load)
        summary = py_interop_summary.run_summary()
        py_interop_summary.summarize_run_metrics(run_metrics, summary)
        q_30_score = round(float(summary.total_summary().percent_gt_q30()),2)

How can I obtain cluster density (K/mm2) and Clusters PF % similarly. The run_summary() module does not give this information. There is another class in the py_interop_metrics which gives these two metrics however I can not figure it out.

dir(py_interop_metrics.tile_metric())        **cluster_density_k, and percent_pf**

When I try to replicate the q30 score code it gives me error:

valid_to_load = py_interop_run.uchar_vector(py_interop_run.Tile, 0)
py_interop_run_metrics.list_summary_metrics_to_load(valid_to_load)
run_folder = run_metrics.read(r"input_dir_path", valid_to_load)
pf_summary = py_interop_metrics.tile_metric()
py_interop_summary.summarize_run_metrics(run_metrics, summary)
py_interop_summary.summarize_run_metrics(run_metrics, pf_summary)

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\\Python\Python311\site-packages\interop\py_interop_summary.py", line 711, in summarize_run_metrics
    return _py_interop_summary.summarize_run_metrics(metrics, summary, skip_median, trim)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: Wrong number or type of arguments for overloaded function 'summarize_run_metrics'.
  Possible C/C++ prototypes are:
    illumina::interop::logic::summary::summarize_run_metrics(illumina::interop::model::metrics::run_metrics &,illumina::interop::model::summary::run_summary &,bool const,bool const)
    illumina::interop::logic::summary::summarize_run_metrics(illumina::interop::model::metrics::run_metrics &,illumina::interop::model::summary::run_summary &,bool const)
    illumina::interop::logic::summary::summarize_run_metrics(illumina::interop::model::metrics::run_metrics &,illumina::interop::model::summary::run_summary &)

Would highly appreciate help, thanks !

Answer 1

[kspata]

I used following commands to calculate Cluster PF % and Cluster Density (K/mm2)

perc_clusters_pf = round(float((summary.at(1).at(0)).percent_pf().mean()),2)
density = round(float((summary.at(1).at(0)).density().mean()),2)
cluster_density = round((density / 1000), 2)  

summary.at(read).at(lane)