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annotate gaiac_precision_calculation/gaiac_precision_calculation.py @ 0:287d6cc86582 draft

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planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
author jay
date Thu, 15 May 2025 14:45:45 +0000
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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1 import scipy
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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2 import argparse
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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3 from scipy.stats.distributions import chi2
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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4 import pandas as pd
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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5 import numpy as np
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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7 def Precision(infile, clm1, clm2, Out):
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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9 df = pd.read_csv(infile, sep="\t")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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10 lOc = int(df.shape[0])
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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12 cl = df.columns.tolist()
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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14 df['PM10_OPC_DIFF']=(((df[cl[int(clm1)-1]])-(df[cl[int(clm2)-1]]))/(((df[cl[int(clm1)-1]])+(df[cl[int(clm2)-1]]))/2)*100)
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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15 df['PM10_OPC_DIFFs']=(df['PM10_OPC_DIFF'])*(df['PM10_OPC_DIFF'])
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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16 d10=df.PM10_OPC_DIFF.sum()
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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17 d10_2=df.PM10_OPC_DIFFs.sum()
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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18 CV_10= (np.sqrt((lOc*(d10_2)-(d10)**2)/(2*lOc*(lOc-1))))*(np.sqrt((lOc-1)/(chi2.ppf(0.1, df=lOc))))
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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19 df1 = pd.DataFrame([CV_10], columns=['Percent Precision'])
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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20 df1.round(4).to_csv(Out,sep='\t')
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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22 if __name__=="__main__":
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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24 parser = argparse.ArgumentParser()
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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26 parser.add_argument("-I", "--infile", required=True, default=None, help="Input file")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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27 parser.add_argument("-c1", "--column_1", required=True, default=None, help="First column")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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28 parser.add_argument("-c2", "--column_2", required=True, default=None, help="Second column")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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29 parser.add_argument("-o", "--out", required=True, default=None, help="OutFile")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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30 args = parser.parse_args()
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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32 Precision(args.infile, args.column_1, args.column_2, args.out)