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How to use notcov method in Nose

Best Python code snippet using nose

stats_yacrd.py

Source:stats_yacrd.py

1#!/usr/bin/env python32import sys3import csv4import argparse5from Bio import SeqIO6from Bio.Seq import Seq7from Bio.SeqRecord import SeqRecord8def main(args):9    if args == None:10        args = sys.argv[1:]11    parser = argparse.ArgumentParser()12    parser.add_argument("-c", "--chimeric", required=True, help="chimeric read",13                        type=argparse.FileType('r'))14    parser.add_argument("-y", "--yacrd", required=True, help="yacrd output",15                        type=argparse.FileType('r'))16    args = vars(parser.parse_args(args))17    true_chimeric = set()18    true_not_chimeric = set()19    for read in SeqIO.parse(args["chimeric"], "fasta"):20        if "chimeric" in read.id:21            true_chimeric.add(read.id)22        else:23            true_not_chimeric.add(read.id)24    all_read = true_chimeric | true_not_chimeric25    positif_notcov = set()26    positif_chimeric = set()27    for row in csv.reader(args["yacrd"], delimiter="\t"):28        if row[0] == "Not_covered":29            positif_notcov.add(row[1])30        if row[0] == "Chimeric":31            positif_chimeric.add(row[1])32    negatif = all_read - positif_chimeric33    34    P = len(true_chimeric)35    N = len(true_not_chimeric)36    FN = len(true_chimeric & negatif)37    TN = len(true_not_chimeric & negatif)38    TP = len(true_chimeric & positif_chimeric)39    FP = len(true_not_chimeric & positif_chimeric)40    print("positif", len(true_chimeric))41    print("negatif", len(true_not_chimeric))42    try:43        print("precision : {:.2%}".format(TP / (TP + FP)))44    except ZeroDivisionError:45        print("can't compute precision TP: {} (TP + FP): {}".format(TP, TP + FP))46    47    try:48        print("sensitivity : {:.2%}".format(TP / P))49    except ZeroDivisionError:50        print("can't compute sensitivity TP: {} P: {}".format(TP, P))51    52    try:53        print("specificity : {:.2%}".format(TN / N))54    except ZeroDivisionError:55        print("can't compute specificity TN: {} N: {}".format(TN, N))56if __name__ == "__main__":...

blah.py

Source:blah.py

1def dostuff():2 print('hi')3def notcov():...

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