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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
author iuc
date Tue, 04 Feb 2025 09:11:04 +0000
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031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
iuc
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1 #!/usr/bin/env python
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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2 """
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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3 IPFP Normalisation
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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4 """
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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5 import argparse
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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6 import sys
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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7
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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8 import numpy as np
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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9
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10
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11 def throw_error(msg, exit_code=1):
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12 sys.stderr.write(msg)
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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13 sys.exit(exit_code)
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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16 def ipfp(data, precision=1e-5, maxIterations=50):
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17 """
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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18 Return the normalized version of the input data (matrix) as an ndarray
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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19 :param data: np.ndArray
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20 :param precision: float combined allowed deviation (residual error) of col and row means from TARGET (=1)
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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21 :param maxIterations: int maximum amount of iterations (1x row and 1x col per iteration)
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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22 :return normalizedData: np.ndArray normalized data
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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23 """
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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24 try:
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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25 assert isinstance(data, np.ndarray) and data.dtype in ['float64', 'int64']
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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26 assert precision > 0
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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27 assert isinstance(maxIterations, int) and maxIterations > 0
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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28 except AssertionError:
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29 throw_error("Invalid input parameters. Please check that the input data consists of floats or integers, precision > 0 and maxIterations is a positive integer.")
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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30 # replace zeros with nan
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31 if (data < 0).any():
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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32 throw_error("Negative values detected, only use positive values.")
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33
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34 zeros = (data == 0)
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35 if zeros.any():
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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36 print("Zero values detected; replacing with NA.")
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37 data = data.astype(float)
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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38 data[zeros] = np.nan
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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39
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40 # initialize variables
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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41 Nrows, Ncols = data.shape
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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42 convergenceTrail = np.asarray([np.nan] * (2 * maxIterations))
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43 convergence = np.inf
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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44 normalized_data = data
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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45 TARGET = 1
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46
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47 i = 0 # number of current iteration
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48 # without reshaping the ndarrays, they have shape (x,) (no second value) and the procedure fails.
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49 # main loop; iterates until convergence is reached (i.e., L1-norm below variable <h>) or the maximum number of
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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50 # iteration cycles is surpassed.
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51 while convergence > precision and i < maxIterations:
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52 # fit the rows
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53 Ri = TARGET * np.asarray(1 / np.nanmean(normalized_data, 1)).reshape(Nrows,)
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54 normalized_data = (normalized_data.T * Ri).T
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55
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56 # calculate deviation from column marginals; row deviation is zero at even indices. (index start = 0)
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57 convergenceTrail[2 * i] = Nrows * 0.5 * np.nansum(np.abs(np.nanmean(normalized_data, 0) - TARGET))
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58
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59 # fit the columns
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60 Si = TARGET * np.asarray(1 / np.nanmean(normalized_data, 0)).reshape(Ncols,)
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61 normalized_data *= Si
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62 # calculate deviation from row marginals; column deviation is zero at odd indices. (index start = 0)
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63 convergenceTrail[2 * i + 1] = Ncols * 0.5 * np.nansum(np.abs(np.nanmean(normalized_data, 1) - TARGET))
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64
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65 convergence = convergenceTrail[2 * i + 1]
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66 i += 1
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67
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68 if i == maxIterations:
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69 throw_error(f"Max number of IPFP iterations ({maxIterations}) reached. Attained precision: {convergence}.")
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70
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71 return normalized_data
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73
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74 def main():
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75 parser = argparse.ArgumentParser(description="IPFP Normalisation")
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76 parser.add_argument('-i', '--input', help="Input file", required=True, metavar="FILE")
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77 parser.add_argument('-p', '--precision', help="Precision", default=1e-5, type=float)
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78 parser.add_argument('-m', '--maxIterations', help="Max iterations", default=50, type=int)
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79 parser.add_argument('-s', '--skipHeaders', help="Skip headers, skips the first n lines", default=0, type=int)
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80
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81 args = parser.parse_args()
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82
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83 try:
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84 data = np.genfromtxt(args.input, skip_header=args.skipHeaders, filling_values=np.nan, delimiter='\t')
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85 normalized_data = ipfp(data, args.precision, args.maxIterations)
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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86 np.savetxt("output.tsv", normalized_data, delimiter='\t')
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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87
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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88 except Exception as e:
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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89 throw_error(str(e))
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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90
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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91
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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92 if __name__ == "__main__":
031cf9d49c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
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93 main()