Mercurial > repos > bebatut > compare_humann2_output

annotate compare_humann2_output.py @ 2:05766022dfc4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
author bebatut
date Mon, 14 Sep 2020 13:50:30 +0000
parents 9959fa526f1a
children eaa95ea1195c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
1 #!/usr/bin/env python
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
2 # -*- coding: utf-8 -*-
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
3
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
4 import argparse
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
5
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
6
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
7 def extract_abundances(fp, nb_charact_to_extract):
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
8 abundances = {}
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
9 more_abund_charact = []
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
10 abund_sum = 0
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
11 with open(fp, 'r') as abundance_f:
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
12 for line in abundance_f.readlines()[1:]:
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
13 split_line = line[:-1].split('\t')
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
14 charact_id = split_line[0]
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
15 abund = float(split_line[1])
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
16 abundances[charact_id] = 100*abund
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
17 abund_sum += abundances[charact_id]
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
18
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
19 if len(more_abund_charact) < nb_charact_to_extract:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
20 more_abund_charact.append(charact_id)
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
21 else:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
22 best_pos = None
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
23 for i in range(len(more_abund_charact)-1, -1, -1):
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
24 if abundances[more_abund_charact[i]] < abund:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
25 best_pos = i
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
26 else:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
27 break
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
28 if best_pos is not None:
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
29 tmp_more_abund_charact = more_abund_charact
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
30 more_abund_charact = tmp_more_abund_charact[:best_pos]
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
31 more_abund_charact += [charact_id]
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
32 more_abund_charact += tmp_more_abund_charact[best_pos:-1]
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
33 return abundances, more_abund_charact
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
34
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
35
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
36 def format_characteristic_name(all_name):
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
37 if all_name.find(':') != -1:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
38 charact_id = all_name.split(':')[0]
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
39 char_name = all_name.split(':')[1][1:]
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
40 else:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
41 charact_id = all_name
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
42 char_name = ''
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
43
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
44 char_name = char_name.replace('/', ' ')
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
45 char_name = char_name.replace('-', ' ')
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
46 char_name = char_name.replace("'", '')
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
47 if char_name.find('(') != -1 and char_name.find(')') != -1:
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
48 open_bracket = char_name.find('(')
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
49 close_bracket = char_name.find(')')+1
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
50 char_name = char_name[:open_bracket] + char_name[close_bracket:]
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
51 return charact_id, char_name
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
52
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
53
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
54 def write_more_abundant_charat(abundances, more_abund_charact, output_fp):
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
55 with open(output_fp, 'w') as output_f:
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
56 output_f.write('id\tname\t%s\n' % '\t'.join(abundances.keys()))
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
57
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
58 for mac in more_abund_charact:
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
59 charact_id, charact_name = format_characteristic_name(mac)
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
60 output_f.write('%s\t%s' % (charact_id, charact_name))
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
61 for sample in abundances:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
62 abund = abundances[sample].get(mac, 0)
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
63 output_f.write('\t%s' % (abund))
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
64 output_f.write('\n')
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
65
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
66
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
67 def extract_similar_characteristics(abund, sim_output_fp, output_files):
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
68 abund_keys = list(abund)
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
69 sim_characteristics = set(abund[abund_keys[0]].keys())
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
70 for sample in abund_keys[1:]:
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
71 sim_characteristics.intersection_update(abund[sample].keys())
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
72 print('Similar between all samples: %s' % len(sim_characteristics))
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
73
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
74 with open(sim_output_fp, 'w') as sim_output_f:
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
75 sim_output_f.write('id\tname\t%s\n' % '\t'.join(abund_keys))
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
76 for charact in list(sim_characteristics):
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
77 charact_id, charact_name = format_characteristic_name(charact)
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
78 sim_output_f.write('%s\t%s' % (charact_id, charact_name))
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
79 for sample in abund_keys:
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
80 sim_output_f.write('\t%s' % abund[sample][charact])
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
81 sim_output_f.write('\n')
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
82
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
83 print('Specific to samples:')
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
84 diff_char = {}
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
85 for i in range(len(abund_keys)):
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
86 sample = abund_keys[i]
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
87 print(' %s' % sample )
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
88 print(' All: %s' % len(abund[sample].keys()))
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
89 diff_char[sample] = set(abund[sample].keys())
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
90 diff_char[sample].difference_update(sim_characteristics)
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
91 perc = 100*len(diff_char[sample])/(1.*len(abund[sample].keys()))
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
92 print(' Number of specific characteristics: %s' % len(diff_char[sample]))
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
93 print(' Percentage of specific characteristics: %s' % perc)
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
94
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
95 relative_abundance = 0
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
96 with open(output_files[i], 'w') as output_f:
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
97 output_f.write('id\tname\tabundances\n')
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
98 for charact in list(diff_char[sample]):
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
99 charact_id, charact_name = format_characteristic_name(charact)
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
100 output_f.write('%s\t%s' % (charact_id, charact_name))
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
101 output_f.write('%s\n' % abund[sample][charact])
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
102 relative_abundance += abund[sample][charact]
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
103 print(' Relative abundance of specific characteristics: %s' % relative_abundance)
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
104
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
105 return sim_characteristics
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
106
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
107
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
108 def compare_humann2_output(args):
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
109 abund = {}
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
110 more_abund_charact = []
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
111
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
112 for i in range(len(args.sample_name)):
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
113 abund[args.sample_name[i]], mac = extract_abundances(
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
114 args.charact_input_fp[i],
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
115 args.most_abundant_characteristics_to_extract)
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
116 more_abund_charact += mac
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
117
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
118 write_more_abundant_charat(
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
119 abund,
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
120 list(set(more_abund_charact)),
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
121 args.more_abundant_output_fp)
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
122 extract_similar_characteristics(
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
123 abund,
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
124 args.similar_output_fp,
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
125 args.specific_output_fp)
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
126
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
127
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
128 if __name__ == '__main__':
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
129 parser = argparse.ArgumentParser()
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
130 parser.add_argument('--sample_name', required=True, action='append')
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
131 parser.add_argument('--charact_input_fp', required=True, action='append')
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
132 parser.add_argument(
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
133 '--most_abundant_characteristics_to_extract',
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
134 required=True,
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
135 type=int)
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
136 parser.add_argument('--more_abundant_output_fp', required=True)
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
137 parser.add_argument('--similar_output_fp', required=True)
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
138 parser.add_argument(
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
139 '--specific_output_fp',
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
140 required=True,
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
141 action='append')
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
142 args = parser.parse_args()
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
143
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
144 if len(args.sample_name) != len(args.charact_input_fp):
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
145 string = "Same number of values (in same order) are expected for "
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
146 string += "--sample_name and --charact_input_fp"
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
147 raise ValueError(string)
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
148 if len(args.sample_name) != len(args.specific_output_fp):
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
149 string = "Same number of values (in same order) are expected for "
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
150 string += "--sample_name and --specific_output_fp"
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
151 raise ValueError(string)
0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
bebatut
parents:
diff changeset
152
2
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
bebatut
parents: 0
diff changeset
153 compare_humann2_output(args)