Mercurial > repos > iuc > ipfp_normalisation
changeset 0:8b5e4ea144a5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation commit 1facbf5b9d74f0f7cd1f9346acb405a2e327c639
| author | iuc |
|---|---|
| date | Tue, 04 Feb 2025 09:11:16 +0000 |
| parents | |
| children | |
| files | ipfp_normalisation.py ipfp_normalisation.xml test-data/bad-input/input.tsv test-data/medium-input/input.tsv test-data/medium-input/output.tsv test-data/nan-input/input.tsv test-data/nan-input/output.tsv test-data/skip-headers/input.tsv test-data/skip-headers/output.tsv test-data/small-input/input.tsv test-data/small-input/output.tsv |
| diffstat | 11 files changed, 596 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipfp_normalisation.py Tue Feb 04 09:11:16 2025 +0000 @@ -0,0 +1,93 @@ +#!/usr/bin/env python +""" +IPFP Normalisation +""" +import argparse +import sys + +import numpy as np + + +def throw_error(msg, exit_code=1): + sys.stderr.write(msg) + sys.exit(exit_code) + + +def ipfp(data, precision=1e-5, maxIterations=50): + """ + Return the normalized version of the input data (matrix) as an ndarray + :param data: np.ndArray + :param precision: float combined allowed deviation (residual error) of col and row means from TARGET (=1) + :param maxIterations: int maximum amount of iterations (1x row and 1x col per iteration) + :return normalizedData: np.ndArray normalized data + """ + try: + assert isinstance(data, np.ndarray) and data.dtype in ['float64', 'int64'] + assert precision > 0 + assert isinstance(maxIterations, int) and maxIterations > 0 + except AssertionError: + throw_error("Invalid input parameters. Please check that the input data consists of floats or integers, precision > 0 and maxIterations is a positive integer.") + # replace zeros with nan + if (data < 0).any(): + throw_error("Negative values detected, only use positive values.") + + zeros = (data == 0) + if zeros.any(): + print("Zero values detected; replacing with NA.") + data = data.astype(float) + data[zeros] = np.nan + + # initialize variables + Nrows, Ncols = data.shape + convergenceTrail = np.asarray([np.nan] * (2 * maxIterations)) + convergence = np.inf + normalized_data = data + TARGET = 1 + + i = 0 # number of current iteration + # without reshaping the ndarrays, they have shape (x,) (no second value) and the procedure fails. + # main loop; iterates until convergence is reached (i.e., L1-norm below variable <h>) or the maximum number of + # iteration cycles is surpassed. + while convergence > precision and i < maxIterations: + # fit the rows + Ri = TARGET * np.asarray(1 / np.nanmean(normalized_data, 1)).reshape(Nrows,) + normalized_data = (normalized_data.T * Ri).T + + # calculate deviation from column marginals; row deviation is zero at even indices. (index start = 0) + convergenceTrail[2 * i] = Nrows * 0.5 * np.nansum(np.abs(np.nanmean(normalized_data, 0) - TARGET)) + + # fit the columns + Si = TARGET * np.asarray(1 / np.nanmean(normalized_data, 0)).reshape(Ncols,) + normalized_data *= Si + # calculate deviation from row marginals; column deviation is zero at odd indices. (index start = 0) + convergenceTrail[2 * i + 1] = Ncols * 0.5 * np.nansum(np.abs(np.nanmean(normalized_data, 1) - TARGET)) + + convergence = convergenceTrail[2 * i + 1] + i += 1 + + if i == maxIterations: + throw_error(f"Max number of IPFP iterations ({maxIterations}) reached. Attained precision: {convergence}.") + + return normalized_data + + +def main(): + parser = argparse.ArgumentParser(description="IPFP Normalisation") + parser.add_argument('-i', '--input', help="Input file", required=True, metavar="FILE") + parser.add_argument('-p', '--precision', help="Precision", default=1e-5, type=float) + parser.add_argument('-m', '--maxIterations', help="Max iterations", default=50, type=int) + parser.add_argument('-s', '--skipHeaders', help="Skip headers, skips the first n lines", default=0, type=int) + + args = parser.parse_args() + + try: + data = np.genfromtxt(args.input, skip_header=args.skipHeaders, filling_values=np.nan, delimiter='\t') + normalized_data = ipfp(data, args.precision, args.maxIterations) + np.savetxt("output.tsv", normalized_data, delimiter='\t') + + except Exception as e: + throw_error(str(e)) + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipfp_normalisation.xml Tue Feb 04 09:11:16 2025 +0000 @@ -0,0 +1,92 @@ +<tool id="ipfp_norm" name="IPFP Normalisation" version="0.1.0+galaxy0" profile="21.05"> + <requirements> + <requirement type="package" version="2.2.2">numpy</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '${__tool_directory__}/ipfp_normalisation.py' + --input '$input' + + #if $precision: + --precision $precision + #end if + + #if $maxIterations: + --maxIterations $maxIterations + #end if + + #if $skipHeaders: + --skipHeaders $skipHeaders + #end if + + ]]></command> + <inputs> + <param argument="--input" type="data" format="tsv" label="input" help="Input file"/> + <param argument="--precision" type="float" value="1e-05" optional="true" label="precision" help="Precision"/> + <param argument="--maxIterations" type="integer" value="50" optional="true" label="maxIterations" help="Max iterations"/> + <param argument="--skipHeaders" type="integer" value="0" optional="true" label="skipHeaders" help="Skips the first n lines to skip headers"/> + </inputs> + <outputs> + <data name="output" from_work_dir="output.tsv" format="tsv" /> + </outputs> + <tests> + <test> + <param name="input" value="small-input/input.tsv"/> + <output name="output" file="small-input/output.tsv" /> + </test> + <test> + <param name="input" value="medium-input/input.tsv"/> + <param name="precision" value="1e-08"/> + <param name="maxIterations" value="100"/> + <output name="output" file="medium-input/output.tsv" /> + </test> + <!-- Skip headers --> + <test> + <param name="input" value="skip-headers/input.tsv"/> + <param name="skipHeaders" value="1"/> + <output name="output" file="skip-headers/output.tsv" /> + </test> + <!-- Unrealistic precision for the amount of iterations --> + <test expect_failure="true"> + <param name="input" value="small-input/input.tsv"/> + <param name="precision" value="1e-20"/> + <param name="maxIterations" value="20"/> + </test> + <!-- Invalid precision --> + <test expect_failure="true"> + <param name="input" value="small-input/input.tsv"/> + <param name="precision" value="-0.1"/> + </test> + <!-- Invalid maxIterations --> + <test expect_failure="true"> + <param name="input" value="small-input/input.tsv"/> + <param name="maxIterations" value="-1"/> + </test> + <!-- Negative number in input --> + <test expect_failure="true"> + <param name="input" value="bad-input/input.tsv"/> + </test> + </tests> + <help><![CDATA[ + This tool normalises a matrix using the Iterative Proportional Fitting Procedure (IPFP). + + The tool takes a matrix consisting of only positive floating point numbers/integers as input and returns the normalized matrix. + + The tool requires a tsv file as input. + + Example input: + input.tsv: + ``` + col1 col2 col3 + 1.321 3.1023 0.9324 + 0.0239 1.1045 0.8301 + 0.1234 0.4312 1.2345 + ... ... ... + ``` + precision: 1e-05 + maxIterations: 50 + skipHeaders: 1 (skips the first line, which are the headers) + ]]></help> + <citations> + <citation type="doi">10.1016/j.jmb.2021.166966</citation> + </citations> +</tool> \ No newline at end of file
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nan-input/input.tsv Tue Feb 04 09:11:16 2025 +0000 @@ -0,0 +1,30 @@ +4.231400670701204181e-01 6.972447935264126651e-01 1.168054985456667971e-02 +9.560556187078717016e-01 2.704180857650853032e-01 8.541409196649117908e-01 +4.276850068211504041e-01 1.551188174921825924e-01 7.564537460025996252e-01 +2.056109152934415540e-01 3.914207894942801635e-01 1.753352755596826462e-01 +3.000182557735093791e-01 8.889017433960088033e-01 6.655057545851970069e-01 +9.206693992696912687e-02 9.063987221561853325e-01 7.834031964516821045e-01 +9.020067834652161221e-01 4.038305132455564106e-01 8.041233683026974832e-01 +2.609992689923649190e-01 2.290773132661515499e-01 6.407978862117292840e-01 +4.302979163567077769e-01 5.189164739152933858e-01 7.282046345415423838e-01 +3.727612357259043607e-01 5.382837810102580889e-01 6.259649541607605894e-01 +4.096371524566553290e-01 1.638901913879453609e-01 1.678342163833023148e-01 +2.186558515622157861e-01 5.622065063130399221e-01 2.998133176366933883e-01 +4.992189737025926055e-01 1.039042287249525298e-01 9.419866770406133405e-01 +9.458437407968390831e-01 1.128206041554240535e-01 +4.683732310273942545e-01 7.463684803475290064e-01 6.812850751802099758e-01 +1.433214923169910948e-01 3.374908339553078784e-01 6.092897069787208686e-01 +1.685995744922146322e-01 6.905776573689135223e-01 6.877749185223458461e-01 +2.993897822998040636e-01 5.909985106906043839e-01 5.678634836964767674e-01 +1.508555881146554922e-01 5.982598790549433776e-01 6.545109450209030122e-02 +1.724739676503597163e-01 5.409229376781971022e-01 2.472459999727213420e-01 +6.565667028105197645e-01 9.583626457707581370e-01 3.649899950922246283e-01 +7.426180877158538030e-01 5.220924947800742455e-01 8.818388121134798086e-01 +6.653679005411207159e-01 2.235211047762991621e-01 4.914949879570088553e-01 +5.351554433048275605e-01 7.170776681718373791e-01 5.641381280847517221e-01 +7.644886789172464781e-01 3.440158136066440164e-01 8.953187419474518682e-01 +4.427103390772796354e-01 6.924506590460971500e-01 8.952268703526516935e-01 +6.967418840845805983e-01 1.774238958422759138e-01 5.270121234373810193e-01 +6.721491722408921010e-01 6.784908515221647063e-01 3.976999198521171675e-01 +1.994366196124827129e-01 1.178064990376457288e-01 +1.413991789112177822e-01 6.509831022834017267e-01 3.659049634212959701e-01
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/skip-headers/input.tsv Tue Feb 04 09:11:16 2025 +0000 @@ -0,0 +1,31 @@ +header1 header2 header3 +4.231400670701204181e-01 6.972447935264126651e-01 1.168054985456667971e-02 +9.560556187078717016e-01 2.704180857650853032e-01 8.541409196649117908e-01 +4.276850068211504041e-01 1.551188174921825924e-01 7.564537460025996252e-01 +2.056109152934415540e-01 3.914207894942801635e-01 1.753352755596826462e-01 +3.000182557735093791e-01 8.889017433960088033e-01 6.655057545851970069e-01 +9.206693992696912687e-02 9.063987221561853325e-01 7.834031964516821045e-01 +9.020067834652161221e-01 4.038305132455564106e-01 8.041233683026974832e-01 +2.609992689923649190e-01 2.290773132661515499e-01 6.407978862117292840e-01 +4.302979163567077769e-01 5.189164739152933858e-01 7.282046345415423838e-01 +3.727612357259043607e-01 5.382837810102580889e-01 6.259649541607605894e-01 +4.096371524566553290e-01 1.638901913879453609e-01 1.678342163833023148e-01 +2.186558515622157861e-01 5.622065063130399221e-01 2.998133176366933883e-01 +4.992189737025926055e-01 1.039042287249525298e-01 9.419866770406133405e-01 +9.458437407968390831e-01 1.128206041554240535e-01 5.962479756357473848e-01 +4.683732310273942545e-01 7.463684803475290064e-01 6.812850751802099758e-01 +1.433214923169910948e-01 3.374908339553078784e-01 6.092897069787208686e-01 +1.685995744922146322e-01 6.905776573689135223e-01 6.877749185223458461e-01 +2.993897822998040636e-01 5.909985106906043839e-01 5.678634836964767674e-01 +1.508555881146554922e-01 5.982598790549433776e-01 6.545109450209030122e-02 +1.724739676503597163e-01 5.409229376781971022e-01 2.472459999727213420e-01 +6.565667028105197645e-01 9.583626457707581370e-01 3.649899950922246283e-01 +7.426180877158538030e-01 5.220924947800742455e-01 8.818388121134798086e-01 +6.653679005411207159e-01 2.235211047762991621e-01 4.914949879570088553e-01 +5.351554433048275605e-01 7.170776681718373791e-01 5.641381280847517221e-01 +7.644886789172464781e-01 3.440158136066440164e-01 8.953187419474518682e-01 +4.427103390772796354e-01 6.924506590460971500e-01 8.952268703526516935e-01 +6.967418840845805983e-01 1.774238958422759138e-01 5.270121234373810193e-01 +6.721491722408921010e-01 6.784908515221647063e-01 3.976999198521171675e-01 +1.994366196124827129e-01 1.813519271551978784e-01 1.178064990376457288e-01 +1.413991789112177822e-01 6.509831022834017267e-01 3.659049634212959701e-01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/skip-headers/output.tsv Tue Feb 04 09:11:16 2025 +0000 @@ -0,0 +1,30 @@ +1.238802271994421389e+00 1.732866646331113758e+00 2.833085820906559860e-02 +1.514944051032812045e+00 3.637568581186076400e-01 1.121299335164818833e+00 +1.081771160614414251e+00 3.330718114081009373e-01 1.585157252171595976e+00 +9.029205094212741090e-01 1.459181316086391123e+00 6.378980172935116988e-01 +5.604429290841307365e-01 1.409611682284410250e+00 1.029945223815339705e+00 +1.828481637050317354e-01 1.528157788639554759e+00 1.288993817697919431e+00 +1.416010173105141545e+00 5.381678143696415617e-01 1.045822192809435336e+00 +7.938340709941633655e-01 5.914724827111300653e-01 1.614693565774141248e+00 +8.757106707624776609e-01 8.965012037144599599e-01 1.227788150773085007e+00 +8.293956793813973549e-01 1.016726961264114326e+00 1.153877341990019456e+00 +1.786698179553708687e+00 6.068297147167470706e-01 6.064722893412397564e-01 +6.946554003956029177e-01 1.516233889861913209e+00 7.891105193443078702e-01 +1.094910331778548018e+00 1.934562271395225408e-01 1.711633711931943802e+00 +1.847839700973952448e+00 1.871092855935013732e-01 9.650513388114931868e-01 +8.432066917611433787e-01 1.140662828719055666e+00 1.016130422513758624e+00 +4.600511624003348343e-01 9.196420333058372698e-01 1.620306793007374457e+00 +3.818381442749248511e-01 1.327692126409216966e+00 1.290469578896356717e+00 +7.063553039789411958e-01 1.183680907541539540e+00 1.109963707846808756e+00 +6.347810397359161527e-01 2.137048816821788932e+00 2.281697454829023086e-01 +6.185512860806933189e-01 1.646833064661356927e+00 7.346154107716317272e-01 +1.111245555659131190e+00 1.376965568787809735e+00 5.117887598016794826e-01 +1.162515643424361089e+00 6.938135110730451194e-01 1.143670957135836996e+00 +1.581312944100051299e+00 4.509584571618966975e-01 9.677288191087516367e-01 +9.964018763601419915e-01 1.133398952923437175e+00 8.701991267618354176e-01 +1.275369959546302390e+00 4.871980612105015207e-01 1.237432166428948266e+00 +7.494204334635453657e-01 9.950770697250511665e-01 1.255502480968706980e+00 +1.627934081143535883e+00 3.519160123710210475e-01 1.020150162551919371e+00 +1.278165088151270723e+00 1.095285401268141445e+00 6.265494987405105798e-01 +1.326665371441246633e+00 1.024096033361061808e+00 6.492386100591159837e-01 +4.254021256813869112e-01 1.662587472420029799e+00 9.120101447959347851e-01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small-input/input.tsv Tue Feb 04 09:11:16 2025 +0000 @@ -0,0 +1,30 @@ +4.231400670701204181e-01 6.972447935264126651e-01 1.168054985456667971e-02 +9.560556187078717016e-01 2.704180857650853032e-01 8.541409196649117908e-01 +4.276850068211504041e-01 1.551188174921825924e-01 7.564537460025996252e-01 +2.056109152934415540e-01 3.914207894942801635e-01 1.753352755596826462e-01 +3.000182557735093791e-01 8.889017433960088033e-01 6.655057545851970069e-01 +9.206693992696912687e-02 9.063987221561853325e-01 7.834031964516821045e-01 +9.020067834652161221e-01 4.038305132455564106e-01 8.041233683026974832e-01 +2.609992689923649190e-01 2.290773132661515499e-01 6.407978862117292840e-01 +4.302979163567077769e-01 5.189164739152933858e-01 7.282046345415423838e-01 +3.727612357259043607e-01 5.382837810102580889e-01 6.259649541607605894e-01 +4.096371524566553290e-01 1.638901913879453609e-01 1.678342163833023148e-01 +2.186558515622157861e-01 5.622065063130399221e-01 2.998133176366933883e-01 +4.992189737025926055e-01 1.039042287249525298e-01 9.419866770406133405e-01 +9.458437407968390831e-01 1.128206041554240535e-01 5.962479756357473848e-01 +4.683732310273942545e-01 7.463684803475290064e-01 6.812850751802099758e-01 +1.433214923169910948e-01 3.374908339553078784e-01 6.092897069787208686e-01 +1.685995744922146322e-01 6.905776573689135223e-01 6.877749185223458461e-01 +2.993897822998040636e-01 5.909985106906043839e-01 5.678634836964767674e-01 +1.508555881146554922e-01 5.982598790549433776e-01 6.545109450209030122e-02 +1.724739676503597163e-01 5.409229376781971022e-01 2.472459999727213420e-01 +6.565667028105197645e-01 9.583626457707581370e-01 3.649899950922246283e-01 +7.426180877158538030e-01 5.220924947800742455e-01 8.818388121134798086e-01 +6.653679005411207159e-01 2.235211047762991621e-01 4.914949879570088553e-01 +5.351554433048275605e-01 7.170776681718373791e-01 5.641381280847517221e-01 +7.644886789172464781e-01 3.440158136066440164e-01 8.953187419474518682e-01 +4.427103390772796354e-01 6.924506590460971500e-01 8.952268703526516935e-01 +6.967418840845805983e-01 1.774238958422759138e-01 5.270121234373810193e-01 +6.721491722408921010e-01 6.784908515221647063e-01 3.976999198521171675e-01 +1.994366196124827129e-01 1.813519271551978784e-01 1.178064990376457288e-01 +1.413991789112177822e-01 6.509831022834017267e-01 3.659049634212959701e-01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small-input/output.tsv Tue Feb 04 09:11:16 2025 +0000 @@ -0,0 +1,30 @@ +1.238802271994421389e+00 1.732866646331113758e+00 2.833085820906559860e-02 +1.514944051032812045e+00 3.637568581186076400e-01 1.121299335164818833e+00 +1.081771160614414251e+00 3.330718114081009373e-01 1.585157252171595976e+00 +9.029205094212741090e-01 1.459181316086391123e+00 6.378980172935116988e-01 +5.604429290841307365e-01 1.409611682284410250e+00 1.029945223815339705e+00 +1.828481637050317354e-01 1.528157788639554759e+00 1.288993817697919431e+00 +1.416010173105141545e+00 5.381678143696415617e-01 1.045822192809435336e+00 +7.938340709941633655e-01 5.914724827111300653e-01 1.614693565774141248e+00 +8.757106707624776609e-01 8.965012037144599599e-01 1.227788150773085007e+00 +8.293956793813973549e-01 1.016726961264114326e+00 1.153877341990019456e+00 +1.786698179553708687e+00 6.068297147167470706e-01 6.064722893412397564e-01 +6.946554003956029177e-01 1.516233889861913209e+00 7.891105193443078702e-01 +1.094910331778548018e+00 1.934562271395225408e-01 1.711633711931943802e+00 +1.847839700973952448e+00 1.871092855935013732e-01 9.650513388114931868e-01 +8.432066917611433787e-01 1.140662828719055666e+00 1.016130422513758624e+00 +4.600511624003348343e-01 9.196420333058372698e-01 1.620306793007374457e+00 +3.818381442749248511e-01 1.327692126409216966e+00 1.290469578896356717e+00 +7.063553039789411958e-01 1.183680907541539540e+00 1.109963707846808756e+00 +6.347810397359161527e-01 2.137048816821788932e+00 2.281697454829023086e-01 +6.185512860806933189e-01 1.646833064661356927e+00 7.346154107716317272e-01 +1.111245555659131190e+00 1.376965568787809735e+00 5.117887598016794826e-01 +1.162515643424361089e+00 6.938135110730451194e-01 1.143670957135836996e+00 +1.581312944100051299e+00 4.509584571618966975e-01 9.677288191087516367e-01 +9.964018763601419915e-01 1.133398952923437175e+00 8.701991267618354176e-01 +1.275369959546302390e+00 4.871980612105015207e-01 1.237432166428948266e+00 +7.494204334635453657e-01 9.950770697250511665e-01 1.255502480968706980e+00 +1.627934081143535883e+00 3.519160123710210475e-01 1.020150162551919371e+00 +1.278165088151270723e+00 1.095285401268141445e+00 6.265494987405105798e-01 +1.326665371441246633e+00 1.024096033361061808e+00 6.492386100591159837e-01 +4.254021256813869112e-01 1.662587472420029799e+00 9.120101447959347851e-01