Mercurial > repos > bebatut > format_metaphlan2_output
annotate format_metaphlan2_output.py @ 1:1e74cb2c8e67 draft
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
author | bebatut |
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date | Mon, 14 Sep 2020 09:52:15 +0000 |
parents | 2bfa9b200600 |
children | 370b56f8a02d |
rev | line source |
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0
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
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1 #!/usr/bin/env python |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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2 # -*- coding: utf-8 -*- |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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3 |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
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4 import argparse |
1
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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5 |
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2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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6 |
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1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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7 taxo_level_corresp = { |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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8 'k': 'kingdom', |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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9 'p': 'phylum', |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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10 'c': 'class', |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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11 'o': 'order', |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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12 'f': 'family', |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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13 'g': 'genus', |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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14 's': 'species', |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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15 't': 'strains'} |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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16 |
0
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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17 |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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18 def write_taxo_abundance(output_files, level, taxo, abundance): |
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1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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19 if level not in taxo_level_corresp: |
0
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
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20 raise ValueError(level + ' is not a know taxonomic level') |
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1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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21 f_n = taxo_level_corresp[level] |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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22 output_files[f_n].write(taxo + '\t') |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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23 output_files[f_n].write(abundance + '\n') |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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24 |
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2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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25 |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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26 def format_metaphlan2_output(args): |
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1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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27 taxo_levels_abund_f = { |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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28 'kingdom': open(args.kingdom_abundance_file, 'w'), |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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29 'phylum': open(args.phylum_abundance_file, 'w'), |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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30 'class': open(args.class_abundance_file, 'w'), |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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31 'order': open(args.order_abundance_file, 'w'), |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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32 'family': open(args.family_abundance_file, 'w'), |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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33 'genus': open(args.genus_abundance_file, 'w'), |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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34 'species': open(args.species_abundance_file, 'w'), |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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35 'strains': open(args.strains_abundance_file, 'w') |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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36 } |
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2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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37 |
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1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
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38 for taxo_level_f in taxo_levels_abund_f: |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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39 s = taxo_level_f + '\t' + 'abundance\n' |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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40 taxo_levels_abund_f[taxo_level_f].write(s) |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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41 |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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42 with open(args.metaphlan2_output, 'r') as input_f: |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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43 with open(args.all_taxo_level_abundance_file, 'w') as output_f: |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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44 s = "kingdom\tphylum\tclass\torder\tfamily\t" |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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45 s += "genus\tspecies\tstrains\tabundance\n" |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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46 output_f.write(s) |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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47 |
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2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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48 levels_number = 8 |
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1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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49 for line in input_f.readlines(): |
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2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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50 if line.startswith("#"): |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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51 continue |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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52 |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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53 split_line = line[:-1].split('\t') |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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54 all_taxo = split_line[0] |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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55 abundance = split_line[1] |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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56 |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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57 split_taxo = all_taxo.split('|') |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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58 for level in split_taxo: |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
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59 taxo = level.split('__')[1] |
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1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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60 taxo = taxo.replace("_", " ") |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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61 output_f.write(taxo + '\t') |
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2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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62 |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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63 for i in range(len(split_taxo), levels_number): |
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1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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64 output_f.write('\t') |
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2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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65 |
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1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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66 output_f.write(abundance + "\n") |
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2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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67 |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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68 last_taxo_level = split_taxo[-1].split('__') |
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1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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69 taxo = last_taxo_level[1].replace("_", " ") |
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2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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70 level = last_taxo_level[0] |
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1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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71 write_taxo_abundance( |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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72 taxo_levels_abund_f, |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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73 level, |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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74 taxo, |
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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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75 abundance) |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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76 |
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"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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77 for taxo_level_f in taxo_levels_abund_f: |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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78 taxo_levels_abund_f[taxo_level_f].close() |
1e74cb2c8e67
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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79 |
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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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80 |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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81 if __name__ == '__main__': |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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82 parser = argparse.ArgumentParser() |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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83 parser.add_argument('--metaphlan2_output', required=True) |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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84 parser.add_argument('--all_taxo_level_abundance_file', required=True) |
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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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85 parser.add_argument('--kingdom_abundance_file', required=True) |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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86 parser.add_argument('--phylum_abundance_file', required=True) |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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87 parser.add_argument('--class_abundance_file', required=True) |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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88 parser.add_argument('--order_abundance_file', required=True) |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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89 parser.add_argument('--family_abundance_file', required=True) |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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90 parser.add_argument('--genus_abundance_file', required=True) |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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91 parser.add_argument('--species_abundance_file', required=True) |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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92 parser.add_argument('--strains_abundance_file', required=True) |
2bfa9b200600
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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93 args = parser.parse_args() |
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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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94 |
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"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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95 format_metaphlan2_output(args) |