comparison qc.py @ 6:878f18249f76 draft

"planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/qc commit 21d348651ca466563cc507b9e3a3fbd6c2b0a016"

5:499b71c93c5d

import csv
import subprocess
import pandas as pd
import matplotlib.pyplot as plt
import shlex

"""
This script can incorporate as many QC checks as required
as long as it outputs a csv file containing a final column
headed with 'qc_pass' and rows for each sample indcating

    with open(args.outfile, 'w') as csvfile:
        header = qc_line.keys()
        writer = csv.DictWriter(csvfile, fieldnames=header)
        writer.writeheader()
        writer.writerow(qc_line)

    N_density = sliding_window_N_density(fasta)
    make_qc_plot(depth_pos, N_density, args.sample)

def main():
    import argparse

6:878f18249f76

import csv
import subprocess
import pandas as pd
import matplotlib.pyplot as plt
import shlex
import json

"""
This script can incorporate as many QC checks as required
as long as it outputs a csv file containing a final column
headed with 'qc_pass' and rows for each sample indcating

    with open(args.outfile, 'w') as csvfile:
        header = qc_line.keys()
        writer = csv.DictWriter(csvfile, fieldnames=header)
        writer.writeheader()
        writer.writerow(qc_line)
    
    # write a json file from the dict
    json_file = args.outfile + '.json'
    with open(args.outfile, 'w') as jsonfile:
       json.dump(qc_line, json_file)
    
    N_density = sliding_window_N_density(fasta)
    make_qc_plot(depth_pos, N_density, args.sample)

def main():
    import argparse