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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/misc commit 94322884bede7ddb9f2a9166952dd0115bdb4e49
author recetox
date Thu, 26 Sep 2024 13:03:05 +0000
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d4c2d5bc0524 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/misc commit 94322884bede7ddb9f2a9166952dd0115bdb4e49
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1 import argparse
d4c2d5bc0524 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/misc commit 94322884bede7ddb9f2a9166952dd0115bdb4e49
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3 import numpy as np
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4 import pandas as pd
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7 def mz_match(marker, peak, ppm):
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8 return np.abs(marker - peak) <= ((peak + marker) / 2) * ppm * 1e-06
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11 def rt_match(marker, peak, tol):
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12 return np.abs(marker - peak) <= tol
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15 def find_matches(peaks, markers, ppm, rt_tol):
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16 # Create a meshgrid of all combinations of mz and rt values
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17 marker_mz = markers['mz'].values[:, np.newaxis]
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18 peak_mz = peaks['mz'].values
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19 marker_rt = markers['rt'].values[:, np.newaxis]
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20 peak_rt = peaks['rt'].values
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22 # Calculate mz and rt matches
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23 mz_matches = mz_match(marker_mz, peak_mz, ppm)
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24 rt_matches = rt_match(marker_rt, peak_rt, rt_tol)
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26 # Find the indices where both mz and rt match
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27 match_indices = np.where(mz_matches & rt_matches)
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29 # Create a DataFrame of hits
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30 matched_markers = markers.iloc[match_indices[0]].reset_index(drop=True)
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31 matched_peaks = peaks.iloc[match_indices[1]].reset_index(drop=True)
d4c2d5bc0524 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/misc commit 94322884bede7ddb9f2a9166952dd0115bdb4e49
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32 hits = pd.concat([matched_markers[['formula']].reset_index(drop=True), matched_peaks], axis=1)
d4c2d5bc0524 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/misc commit 94322884bede7ddb9f2a9166952dd0115bdb4e49
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34 # Calculate mz and rt differences
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35 hits['mz_diff'] = np.abs(matched_markers['mz'].values - matched_peaks['mz'].values)
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36 hits['rt_diff'] = np.abs(matched_markers['rt'].values - matched_peaks['rt'].values)
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38 return hits
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41 def main():
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42 parser = argparse.ArgumentParser(description='Find matches between peaks and markers.')
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43 parser.add_argument('--peaks', required=True, help='Path to the peaks parquet file.')
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44 parser.add_argument('--markers', required=True, help='Path to the markers CSV file.')
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45 parser.add_argument('--output', required=True, help='Path to the output TSV file.')
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46 parser.add_argument('--ppm', type=int, default=5, help='PPM tolerance for mz matching.')
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47 parser.add_argument('--rt_tol', type=int, default=10, help='RT tolerance for rt matching.')
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48 args = parser.parse_args()
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50 peaks = pd.read_parquet(args.peaks)
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51 markers = pd.read_csv(args.markers, sep='\t')
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53 hits = find_matches(peaks, markers, args.ppm, args.rt_tol)
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55 hits.to_csv(args.output, sep='\t', index=False)
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58 if __name__ == "__main__":
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59 main()