Install

If you do not have the Python InterOp library installed, then you can do the following:

$ pip install -f https://github.com/Illumina/interop/releases/latest interop

You can verify that InterOp is properly installed:

$ python -m interop --test

Before you begin

If you plan to use this tutorial in an interactive fashion, then you should download an example run folder for an Illumina sequencer. For example, you may download and extract this example run folder: MiSeqDemo

Please change the path below so that it points at the run folder you wish to use:



In [7]:

    
run_folder = r"D:\RTA.Data\InteropData\MiSeqDemo"

How to access a metric at a low level: Extraction Metrics

This section introduces loading and accessing elements of a single metric: ExtractionMetricsOut.bin



In [8]:

    
from interop import py_interop_run_metrics, py_interop_run



In [9]:

    
run_metrics = py_interop_run_metrics.run_metrics()
valid_to_load = py_interop_run.uchar_vector(py_interop_run.MetricCount, 0)



In [10]:

    
valid_to_load[py_interop_run.Extraction]=1



In [11]:

    
run_metrics.read(run_folder, valid_to_load)



In [12]:

    
extraction_metrics = run_metrics.extraction_metric_set()



In [13]:

    
print "Last Cycle: ", extraction_metrics.max_cycle()









    



Last Cycle:  602



In [14]:

    
lane, tile, cycle, channel = (1, 1101, 15, 0)
extraction_metric = extraction_metrics.get_metric(lane, tile, cycle)
intensity = extraction_metric.max_intensity (channel)



In [15]:

    
print "Intensity for channel", channel, " lane", lane, "tile", tile, "cycle", cycle, "is", intensity









    



Intensity for channel 0  lane 1 tile 1101 cycle 15 is 220



In [16]:

    
extraction_metric = extraction_metrics.at(0)
intensity = extraction_metric.max_intensity (channel)



In [17]:

    
print "Intensity for channel", channel, " lane", extraction_metric.lane(), "tile", extraction_metric.tile(), "cycle", extraction_metric.cycle(), "is", intensity









    



Intensity for channel 0  lane 1 tile 1101 cycle 1 is 249



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