Mercurial > repos > thanhlv > humann3

annotate test-data/test-db/metaphlan-db/customizemapping.py @ 1:469b5fe416ad draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
author thanhlv
date Tue, 14 Feb 2023 11:15:40 +0000
parents ab86614989fd
children
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ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
1 #!/usr/bin/env python
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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2 # -*- coding: utf-8 -*-
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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3 # Script to generate a extract a custom mapping file from input mapping file.
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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4 # Mostly used for a reduced-size demo data generation.
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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5
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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6
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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7 import argparse
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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8 from pathlib import Path
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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9
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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11 if __name__ == '__main__':
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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12 # Read command line
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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13 parser = argparse.ArgumentParser(description='Customize HUMAnN utility mapping')
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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14 parser.add_argument('--in_mapping', help="Path to mapping file to reduce")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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15 parser.add_argument('--features', help="Path to tabular file with features to keep in first column")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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16 parser.add_argument('--elements', help="Path to tabular file with elements to keep in other columns")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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17 parser.add_argument('--out_mapping', help="Path to reduced mapping file")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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18 args = parser.parse_args()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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19
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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20 in_mapping_fp = Path(args.in_mapping)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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21 feature_fp = Path(args.features)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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22 element_fp = Path(args.elements)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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23 out_mapping_fp = Path(args.out_mapping)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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24
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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25 # extract features to keep
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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26 features = set()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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27 with open(feature_fp, 'r') as feature_f:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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28 for line in feature_f.readlines():
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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29 features.add(line.split("\t")[0])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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30 print(features)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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31
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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32 # extract elements to keep
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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33 elements = set()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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34 with open(element_fp, 'r') as element_f:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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35 for line in element_f.readlines():
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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36 elements.add(line.split("\t")[0])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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37 print(elements)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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38
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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39 # write mapping for features to keep while keeping only elements
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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40 with open(in_mapping_fp, 'r') as in_mapping_f:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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41 with open(out_mapping_fp, 'w') as out_mapping_f:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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42 for line in in_mapping_f.readlines():
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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43 l_split = line.split("\t")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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44 feat = l_split[0]
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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45 if feat in features:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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46 to_write = [feat]
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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47 for e in l_split[1:]:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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48 if e in elements:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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49 to_write.append(e)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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50 out_mapping_f.write("%s\n" % '\t'.join(to_write))