Mercurial > repos > iuc > heinz
annotate heinz_scoring.py @ 1:5f589c91566e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author | iuc |
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date | Tue, 30 Oct 2018 18:57:02 -0400 |
parents | e41ec5af7472 |
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rev | line source |
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e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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1 #!/usr/bin/env python |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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2 """Calculate scores for Heinz. |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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3 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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4 This script transform a p-value into a score: |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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5 1. Use alpha and lambda to calculate a threshold P-value. |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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6 2. Calculate a score based on each P-value by alpha and the threshold. |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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7 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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8 For more details, please refer to the paper doi:10.1093/bioinformatics/btn161 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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9 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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10 Input: |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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11 P-values from DESeq2 result: first column: names, second column P-values |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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12 Output: |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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13 Scores, which will be used as the input of Heinz. |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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14 First column: names, second column: scores. |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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15 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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16 Python 3 is required. |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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17 """ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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18 # Implemented by: Chao (Cico) Zhang |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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19 # Homepage: https://Hi-IT.org |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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20 # Date: 14 Mar 2017 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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21 # Last modified: 23 May 2018 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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22 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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23 import argparse |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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24 import sys |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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25 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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26 import numpy as np |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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27 import pandas as pd |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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28 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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29 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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30 parser = argparse.ArgumentParser(description='Transform a P-value into a ' |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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31 'score which can be used as the input of ' |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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32 'Heinz') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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33 parser.add_argument('-n', '--node', required=True, dest='nodes', |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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34 metavar='nodes_pvalue.txt', type=str, |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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35 help='Input file of nodes with P-values') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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36 parser.add_argument('-f', '--fdr', required=True, dest='fdr', |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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37 metavar='0.007', type=float, help='Choose a value of FDR') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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38 parser.add_argument('-m', '--model', required=False, dest='param_file', |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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39 metavar='param.txt', type=str, |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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40 help='A txt file contains model params as input') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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41 parser.add_argument('-a', '--alpha', required=False, dest='alpha', |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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42 metavar='0.234', type=float, default=0.5, |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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43 help='Single parameter alpha as input if txt input is ' |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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44 'not provided') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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45 parser.add_argument('-l', '--lambda', required=False, dest='lam', |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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46 metavar='0.345', type=float, default=0.5, |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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47 help='Single parameter lambda as input if txt input is ' |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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48 'not provided') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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49 parser.add_argument('-o', '--output', required=True, dest='output', |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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50 metavar='scores.txt', type=str, |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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51 help='The output file to store the calculated scores') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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52 args = parser.parse_args() |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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53 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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54 # Check if the parameters are complete |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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55 if args.output is None: |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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56 sys.exit('Output file is not designated.') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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57 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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58 if args.nodes is None: |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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59 sys.exit('Nodes with p-values must be provided.') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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60 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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61 if args.fdr is None: |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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62 sys.exit('FDR must be provided') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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63 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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64 if args.fdr >= 1 or args.fdr <= 0: |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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65 sys.exit('FDR must greater than 0 and smaller than 1') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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66 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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67 # run heinz-print according to the input type |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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68 if args.param_file is not None: # if BUM output is provided |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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69 with open(args.param_file) as p: |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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70 params = p.readlines() |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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71 lam = float(params[0]) # Maybe this is a bug |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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72 alpha = float(params[1]) # Maybe this is a bug |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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73 # if BUM output is not provided |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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74 elif args.alpha is not None and args.lam is not None: |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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75 lam = args.lam |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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76 alpha = args.alpha |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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77 else: # The input is not complete |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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78 sys.exit('The parameters of the model are incomplete.') |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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79 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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80 # Calculate the threshold P-value |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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81 pie = lam + (1 - lam) * alpha |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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82 p_threshold = np.power((pie - lam * args.fdr) / (args.fdr - lam * args.fdr), |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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83 1 / (alpha - 1)) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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84 print(p_threshold) |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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85 # Calculate the scores |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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86 input_pvalues = pd.read_csv(args.nodes, sep='\t', names=['node', 'pvalue']) |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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87 input_pvalues.loc[:, 'score'] = input_pvalues.pvalue.apply(lambda x: |
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5f589c91566e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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88 (alpha - 1) * (np.log(x) - np.log(p_threshold))) |
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e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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89 # print(input_pvalues.loc[:, ['node', 'score']]) |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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90 input_pvalues.loc[:, ['node', 'score']].to_csv(args.output, sep='\t', |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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91 index=False, header=False) |