Question: parsing run info data with Interop
0
gravatar for genya35
5 weeks ago by
genya3530
genya3530 wrote:

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 • 132 views
ADD COMMENTlink written 5 weeks ago by genya3530
0
gravatar for genomax
5 weeks ago by
genomax89k
United States
genomax89k wrote:

See answer here: A: Parser for Illumina Novaseq metadata

ADD COMMENTlink written 5 weeks ago by genomax89k

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

ADD REPLYlink written 4 weeks ago by genya3530
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