This is a test version of Biostars. For the public version, visit https://www.biostars.org.
parsing run info data with Interop

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

1 answer

See answer here: A: Parser for Illumina Novaseq metadata

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

Log in to answer this question.