ezralanglois

import interop.core
import pandas

'''
NovaSeq run: 10x Genomics Single Cell 3' Gene Expression

10x Genomics 3’ Gene Expression libraries (dual index) were generated from ~1200 PBMC cells as described in 
the CG000315 - Chromium Next GEMSingle Cell 3ʹ Reagent Kits v3.1 (Dual Index) Rev C. 8 individual 10X Gene 
Expression libraries (technical replicates) were sequenced in the 10x Genomics lab on a NovaSeq 6000 using the SP flowcell.

ezralanglois

# Tested with 
#  - Anaconda Python 3.7
#  - Illumina InterOp 1.1.12

import interop.py_interop_plot as interop_plot
import interop.py_interop_run as interop_run
import interop.py_interop_run_metrics as interop_run_metrics
import pandas as pd

ezralanglois

from interop import py_interop_run_metrics, py_interop_run, py_interop_plot
import matplotlib.pyplot as plt

# Read in InterOp Data
run_folder = r"D:\RTA.Data\InteropData\MiSeqDemo"
run_metrics = py_interop_run_metrics.run_metrics()
valid_to_load = py_interop_run.uchar_vector(py_interop_run.MetricCount, 0)
valid_to_load[py_interop_run.Q]=1
run_metrics.read(run_folder, valid_to_load)

ezralanglois

/** Populate and use a Q-metric Set
 *
 *
 *  @file
 *  @date 4/6/17
 *  @version 1.0
 *  @copyright Illumina Use Only
 */

#include <iostream>

ezralanglois

#include "interop/model/metric_sets/extraction_metric_set.h"
#include "interop/io/metric_file_stream.h"

using namespace illumina::interop::model::metrics;
using namespace illumina::interop::io;

void first_cycle_intensity_by_lane(const extraction_metrics& extraction_metric_set, std::map<  size_t, float >& intensity_by_lane )
{
    const size_t channel = 0;
    std::map<  size_t, size_t > count_by_lane;