parsing run info data with Interop
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15 months ago
genya35 ▴ 40

Hello,

I'm learning how to parse Illumina NGS data with Interop and Python. I've read the tutorials but still confused which function to use to get 'Run Info' stats (http://illumina.github.io/interop/group__run__info.html). For example, how to get 'instrument_name ()' and 'flowcell_id ()'. I understand that these are part of 'run_metrics' class but not sure how to access them correctly.

run_folder = r"/path/to/run/folder"
from interop import py_interop_run_metrics, py_interop_run, py_interop_summary

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)
#incorrect
instrument_name = run_metrics.instrument_name()
print "instrument name: ", instrument_name

Thanks for your help in advance.

next-gen • 712 views
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Entering edit mode
15 months ago
GenoMax 110k

See answer here: A: Parser for Illumina Novaseq metadata

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Thanks, that is very helpful. I just need to understand how to get the 'total yield' from that file.

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