Mercurial > repos > bebatut > format_metaphlan2_output
comparison format_metaphlan2_output.py @ 2:370b56f8a02d draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
author | bgruening |
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date | Wed, 19 Oct 2022 14:39:16 +0000 |
parents | 1e74cb2c8e67 |
children |
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1:1e74cb2c8e67 | 2:370b56f8a02d |
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3 | 3 |
4 import argparse | 4 import argparse |
5 | 5 |
6 | 6 |
7 taxo_level_corresp = { | 7 taxo_level_corresp = { |
8 'k': 'kingdom', | 8 "k": "kingdom", |
9 'p': 'phylum', | 9 "p": "phylum", |
10 'c': 'class', | 10 "c": "class", |
11 'o': 'order', | 11 "o": "order", |
12 'f': 'family', | 12 "f": "family", |
13 'g': 'genus', | 13 "g": "genus", |
14 's': 'species', | 14 "s": "species", |
15 't': 'strains'} | 15 "t": "strains", |
16 | 16 } |
17 | |
17 | 18 |
18 def write_taxo_abundance(output_files, level, taxo, abundance): | 19 def write_taxo_abundance(output_files, level, taxo, abundance): |
19 if level not in taxo_level_corresp: | 20 if level not in taxo_level_corresp: |
20 raise ValueError(level + ' is not a know taxonomic level') | 21 raise ValueError(level + " is not a know taxonomic level") |
21 f_n = taxo_level_corresp[level] | 22 f_n = taxo_level_corresp[level] |
22 output_files[f_n].write(taxo + '\t') | 23 output_files[f_n].write(taxo + "\t") |
23 output_files[f_n].write(abundance + '\n') | 24 output_files[f_n].write(abundance + "\n") |
24 | 25 |
25 | 26 |
26 def format_metaphlan2_output(args): | 27 def format_metaphlan2_output(args): |
27 taxo_levels_abund_f = { | 28 taxo_levels_abund_f = { |
28 'kingdom': open(args.kingdom_abundance_file, 'w'), | 29 "kingdom": open(args.kingdom_abundance_file, "w"), |
29 'phylum': open(args.phylum_abundance_file, 'w'), | 30 "phylum": open(args.phylum_abundance_file, "w"), |
30 'class': open(args.class_abundance_file, 'w'), | 31 "class": open(args.class_abundance_file, "w"), |
31 'order': open(args.order_abundance_file, 'w'), | 32 "order": open(args.order_abundance_file, "w"), |
32 'family': open(args.family_abundance_file, 'w'), | 33 "family": open(args.family_abundance_file, "w"), |
33 'genus': open(args.genus_abundance_file, 'w'), | 34 "genus": open(args.genus_abundance_file, "w"), |
34 'species': open(args.species_abundance_file, 'w'), | 35 "species": open(args.species_abundance_file, "w"), |
35 'strains': open(args.strains_abundance_file, 'w') | 36 "strains": open(args.strains_abundance_file, "w"), |
36 } | 37 } |
37 | 38 |
38 for taxo_level_f in taxo_levels_abund_f: | 39 for taxo_level_f in taxo_levels_abund_f: |
39 s = taxo_level_f + '\t' + 'abundance\n' | 40 s = taxo_level_f + "\t" + "abundance\n" |
40 taxo_levels_abund_f[taxo_level_f].write(s) | 41 taxo_levels_abund_f[taxo_level_f].write(s) |
41 | 42 |
42 with open(args.metaphlan2_output, 'r') as input_f: | 43 with open(args.metaphlan2_output, "r") as input_f: |
43 with open(args.all_taxo_level_abundance_file, 'w') as output_f: | 44 with open(args.all_taxo_level_abundance_file, "w") as output_f: |
44 s = "kingdom\tphylum\tclass\torder\tfamily\t" | 45 s = "kingdom\tphylum\tclass\torder\tfamily\t" |
45 s += "genus\tspecies\tstrains\tabundance\n" | 46 s += "genus\tspecies\tstrains\tabundance\n" |
46 output_f.write(s) | 47 output_f.write(s) |
47 | 48 |
48 levels_number = 8 | 49 levels_number = 8 |
49 for line in input_f.readlines(): | 50 for line in input_f.readlines(): |
50 if line.startswith("#"): | 51 if line.startswith("#"): |
51 continue | 52 continue |
52 | 53 |
53 split_line = line[:-1].split('\t') | 54 split_line = line[:-1].split("\t") |
54 all_taxo = split_line[0] | 55 all_taxo = split_line[0] |
55 abundance = split_line[1] | 56 abundance = split_line[1] |
56 | 57 |
57 split_taxo = all_taxo.split('|') | 58 split_taxo = all_taxo.split("|") |
58 for level in split_taxo: | 59 for level in split_taxo: |
59 taxo = level.split('__')[1] | 60 taxo = level.split("__")[1] |
60 taxo = taxo.replace("_", " ") | 61 taxo = taxo.replace("_", " ") |
61 output_f.write(taxo + '\t') | 62 output_f.write(taxo + "\t") |
62 | 63 |
63 for i in range(len(split_taxo), levels_number): | 64 for i in range(len(split_taxo), levels_number): |
64 output_f.write('\t') | 65 output_f.write("\t") |
65 | 66 |
66 output_f.write(abundance + "\n") | 67 output_f.write(abundance + "\n") |
67 | 68 |
68 last_taxo_level = split_taxo[-1].split('__') | 69 last_taxo_level = split_taxo[-1].split("__") |
69 taxo = last_taxo_level[1].replace("_", " ") | 70 taxo = last_taxo_level[1].replace("_", " ") |
70 level = last_taxo_level[0] | 71 level = last_taxo_level[0] |
71 write_taxo_abundance( | 72 write_taxo_abundance(taxo_levels_abund_f, level, taxo, abundance) |
72 taxo_levels_abund_f, | |
73 level, | |
74 taxo, | |
75 abundance) | |
76 | 73 |
77 for taxo_level_f in taxo_levels_abund_f: | 74 for taxo_level_f in taxo_levels_abund_f: |
78 taxo_levels_abund_f[taxo_level_f].close() | 75 taxo_levels_abund_f[taxo_level_f].close() |
79 | 76 |
80 | 77 |
81 if __name__ == '__main__': | 78 if __name__ == "__main__": |
82 parser = argparse.ArgumentParser() | 79 parser = argparse.ArgumentParser() |
83 parser.add_argument('--metaphlan2_output', required=True) | 80 parser.add_argument("--metaphlan2_output", required=True) |
84 parser.add_argument('--all_taxo_level_abundance_file', required=True) | 81 parser.add_argument("--all_taxo_level_abundance_file", required=True) |
85 parser.add_argument('--kingdom_abundance_file', required=True) | 82 parser.add_argument("--kingdom_abundance_file", required=True) |
86 parser.add_argument('--phylum_abundance_file', required=True) | 83 parser.add_argument("--phylum_abundance_file", required=True) |
87 parser.add_argument('--class_abundance_file', required=True) | 84 parser.add_argument("--class_abundance_file", required=True) |
88 parser.add_argument('--order_abundance_file', required=True) | 85 parser.add_argument("--order_abundance_file", required=True) |
89 parser.add_argument('--family_abundance_file', required=True) | 86 parser.add_argument("--family_abundance_file", required=True) |
90 parser.add_argument('--genus_abundance_file', required=True) | 87 parser.add_argument("--genus_abundance_file", required=True) |
91 parser.add_argument('--species_abundance_file', required=True) | 88 parser.add_argument("--species_abundance_file", required=True) |
92 parser.add_argument('--strains_abundance_file', required=True) | 89 parser.add_argument("--strains_abundance_file", required=True) |
93 args = parser.parse_args() | 90 args = parser.parse_args() |
94 | 91 |
95 format_metaphlan2_output(args) | 92 format_metaphlan2_output(args) |