Mercurial > repos > iuc > humann_rename_table
annotate test-data/test-db/metaphlan-db/customizemapping.py @ 6:aabf8cfb8fef draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit cb7dc8ff1810f6d335b5dd6615651f32a3ea7447
author | iuc |
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date | Fri, 27 Sep 2024 09:59:02 +0000 |
parents | 172920f67a84 |
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172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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1 #!/usr/bin/env python |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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2 # -*- coding: utf-8 -*- |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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3 # Script to generate a extract a custom mapping file from input mapping file. |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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4 # Mostly used for a reduced-size demo data generation. |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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5 |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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6 |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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7 import argparse |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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8 from pathlib import Path |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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9 |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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10 |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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11 if __name__ == '__main__': |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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12 # Read command line |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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13 parser = argparse.ArgumentParser(description='Customize HUMAnN utility mapping') |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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14 parser.add_argument('--in_mapping', help="Path to mapping file to reduce") |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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15 parser.add_argument('--features', help="Path to tabular file with features to keep in first column") |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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16 parser.add_argument('--elements', help="Path to tabular file with elements to keep in other columns") |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
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17 parser.add_argument('--out_mapping', help="Path to reduced mapping file") |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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18 args = parser.parse_args() |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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19 |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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20 in_mapping_fp = Path(args.in_mapping) |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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diff
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21 feature_fp = Path(args.features) |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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diff
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22 element_fp = Path(args.elements) |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
diff
changeset
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23 out_mapping_fp = Path(args.out_mapping) |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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diff
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24 |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
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25 # extract features to keep |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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26 features = set() |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
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27 with open(feature_fp, 'r') as feature_f: |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
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changeset
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28 for line in feature_f.readlines(): |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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29 features.add(line.split("\t")[0]) |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
diff
changeset
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30 print(features) |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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31 |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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32 # extract elements to keep |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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33 elements = set() |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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changeset
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34 with open(element_fp, 'r') as element_f: |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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diff
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35 for line in element_f.readlines(): |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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36 elements.add(line.split("\t")[0]) |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
diff
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37 print(elements) |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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38 |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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39 # write mapping for features to keep while keeping only elements |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
diff
changeset
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40 with open(in_mapping_fp, 'r') as in_mapping_f: |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
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41 with open(out_mapping_fp, 'w') as out_mapping_f: |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
diff
changeset
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42 for line in in_mapping_f.readlines(): |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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43 l_split = line.split("\t") |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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44 feat = l_split[0] |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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45 if feat in features: |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
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46 to_write = [feat] |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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47 for e in l_split[1:]: |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
parents:
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48 if e in elements: |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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49 to_write.append(e) |
172920f67a84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
iuc
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50 out_mapping_f.write("%s\n" % '\t'.join(to_write)) |