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annotate gaiac_data_averaging/gaiac_dataaveraging.py @ 3:1f9e67edde6a draft default tip

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planemo upload for repository https://github.com/jaidevjoshi83/gaiac commit e9587f93346c7b55e1be00bad5844bf2db3ed03d-dirty
author jay
date Thu, 10 Jul 2025 19:42:02 +0000
parents 287d6cc86582
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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1 import pandas as pd
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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2 import argparse
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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4 #This tool would average your time series data based on the time intervals based on the time and date column
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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5 #python avg_timeseries.py -I data.tsv -C 1 -T 5 -O averaged_output.tsv
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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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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8 def main():
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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9 parser = argparse.ArgumentParser(description="Average time series data over specified intervals.")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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10 parser.add_argument("-I", "--infile", required=True, help="Input data file (TSV format)")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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11 parser.add_argument("-C", "--dt_column", required=True, help="Column number (1-based) for the DateTime column")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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12 parser.add_argument("-T", "--time_interval", required=True, help="Time interval in minutes, e.g., '5' or '30'")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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13 parser.add_argument("-O", "--out_file", default='OutFile.tsv', help="Output file name (TSV format)")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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14 parser.add_argument("-S", "--sep", default='\t', help="deliminator")
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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16 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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18 # Load data
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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19 data = pd.read_csv(args.infile, sep=args.sep)
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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21 # Extract the correct datetime column name
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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22 col_index = int(args.dt_column) - 1 # Convert 1-based index to 0-based
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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23 datetime_col = data.columns[col_index]
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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25 # Set datetime index
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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26 data[datetime_col] = pd.to_datetime(data[datetime_col], errors='coerce')
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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27 data.set_index(datetime_col, inplace=True)
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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29 # Group by time intervals and compute mean for numeric columns
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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30 df_avg = data.resample(f'{args.time_interval}Min').mean(numeric_only=True)
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 # Round to 3 decimals and save to output file
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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33 df_avg.round(3).to_csv(args.out_file, 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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35 print(f"Averaged data saved to {args.out_file}")
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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37 if __name__ == "__main__":
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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38 main()