Mercurial > repos > thanhlv > humann3

annotate customizemetadata.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
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1 #!/usr/bin/env python
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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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
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3
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4 import argparse
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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5 import bz2
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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6 import json
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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7 import pickle
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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8 import re
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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9 import sys
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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10 from importlib.metadata import version
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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11 from pathlib import Path
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12
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13 from packaging.version import Version
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16 def load_from_json(json_fp):
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17 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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18 Read JSON file with marker metadata
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20 :param json_fp: Path to JSON file
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21 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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22 with open(json_fp, 'r') as json_f:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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23 data = json.load(json_f)
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25 for m in data['markers']:
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26 data['markers'][m]['ext'] = set(data['markers'][m]['ext'])
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28 for t in data['taxonomy']:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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29 if isinstance(data['taxonomy'][t], list):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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30 data['taxonomy'][t] = tuple(data['taxonomy'][t])
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31 return data
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34 def dump_to_json(data, json_fp):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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35 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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36 Dump marker metadata to JSON file
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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37
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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38 :param json_fp: Path to JSON file
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39 '''
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40 for m in data['markers']:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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41 data['markers'][m]['ext'] = list(data['markers'][m]['ext'])
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42
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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43 with open(json_fp, 'w') as json_f:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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44 json.dump(data, json_f)
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45
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46
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47 def transform_pkl_to_json(pkl_fp, json_fp):
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48 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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49 Read Pickle file and drop it to a JSON file
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50
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51 :param pkl_fp: Path to input Pickle file
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52 :param json_fp: Path to output JSON file
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53 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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54 # load metadata from Pickle file
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55 with bz2.BZ2File(pkl_fp, 'r') as pkl_f:
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56 in_metadata = pickle.load(pkl_f)
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57
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58 out_metadata = {
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59 'markers': in_metadata['markers'],
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60 'taxonomy': in_metadata['taxonomy'],
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61 'merged_taxon': {}
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62 }
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63
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64 # transform merged_taxons tuple keys to string
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65 for k in in_metadata['merged_taxon']:
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66 n = ' , '.join(k)
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67 out_metadata[n] = in_metadata['merged_taxon'][k]
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68
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69 # dump metadata to JSON file
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70 dump_to_json(out_metadata, json_fp)
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71
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72
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73 def validate_map_version(infile, file_type):
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74 '''
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75 Check conformity of a user-provided pkl file to Metaphlan SGB (>= v4.0).
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76
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77 :param infile: Path to input Pickle/JSON file
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78 :param file_type: String definining file type, pkl or JSON. Case-insensitive
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79 '''
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80 file_type = file_type.lower()
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81 if file_type == 'pkl' or file_type == 'pickle':
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82 # load metadata from Pickle file
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83 with bz2.BZ2File(infile, 'r') as pkl_f:
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84 in_metadata = pickle.load(pkl_f)
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85 elif file_type == 'json':
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86 in_metadata = load_from_json(infile)
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87 else:
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88 raise ValueError("Unsupported file type to validate.")
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89
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90 # Get metaphlan version in $PATH
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91 metaphlan_version = Version(version('metaphlan'))
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92
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93 # Ensure that there are 8 taxonomy levels separated with "|"s.
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94 # v3 DB release encodes the taxids as: ('2|1224|1236|91347|543|547|354276', 4404432)
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95 # v4 DB release encodes the taxids as: ('2|1224|1236|91347|543|547|354276|', 4404432)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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96 for k in in_metadata['taxonomy']:
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97 if (in_metadata['taxonomy'][k][0].count('|') != 7 and metaphlan_version >= Version('4')) or (in_metadata['taxonomy'][k][0].count('|') != 6 and metaphlan_version < Version('4')):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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98 # raise ValueError("Missing/Extra values in GCA list")
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99 print("The input taxonomy mapping file %s is incompatible with Metaphlan v.%s in $PATH." % (infile, metaphlan_version))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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100 sys.exit(42)
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101
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102 print("%s is compatible with Metaphlan v.%s." % (infile, metaphlan_version))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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103
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104
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105 def transform_json_to_pkl(json_fp, pkl_fp):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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106 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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107 Read JSON file and drop it to a Pickle file
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108
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109 :param json_fp: Path to input JSON file
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110 :param pkl_fp: Path to output Pickle file
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111 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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112 # load metadata from JSON file
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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113 in_metadata = load_from_json(json_fp)
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114
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115 out_metadata = {
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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116 'markers': in_metadata['markers'],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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117 'taxonomy': in_metadata['taxonomy'],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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118 'merged_taxon': {}
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119 }
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120
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121 # transform merged_taxons keys to tuple
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122 for k in in_metadata['merged_taxon']:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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123 n = ' , '.split(k)
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124 out_metadata[n] = in_metadata['merged_taxon'][k]
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125
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126 # dump metadata to Pickle file
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127 with bz2.BZ2File(pkl_fp, 'w') as pkl_f:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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128 pickle.dump(out_metadata, pkl_f)
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129
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130
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131 def add_marker(in_json_fp, out_json_fp, name, m_length, g_length, gca, k_name, k_id, p_name, p_id, c_name, c_id, o_name, o_id, f_name, f_id, g_name, g_id, s_name, s_id, t_name):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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132 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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133 Add marker to JSON file
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134
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135 :param in_json_fp: Path to input JSON file
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136 :param out_json_fp: Path to output JSON file
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137 :param name: Name of new marker
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138 :param m_length: Length of new marker
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139 :param g_length: List with lengths of genomes from which the new marker has been extracted
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140 :param gca: List with GCA of genomes from which the new marker has been extracted
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141 :param k_name: List with Name of Kingdom for genomes from which the new marker has been extracted
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142 :param k_id: List with NCBI id of Kingdom for genomes from which the new marker has been extracted
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143 :param p_name: List with Name of Phylum for genomes from which the new marker has been extracted
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144 :param p_id: List with NCBI id of Phylum for genomes from which the new marker has been extracted
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145 :param c_name: List with Name of Class for genomes from which the new marker has been extracted
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146 :param c_id: List with NCBI id of Class for genomes from which the new marker has been extracted
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147 :param o_name: List with Name of Order for genomes from which the new marker has been extracted
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148 :param o_id: List with NCBI id of Order for genomes from which the new marker has been extracted
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149 :param f_name: List with Name of Family for genomes from which the new marker has been extracted
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150 :param f_id: List with NCBI id of Family for genomes from which the new marker has been extracted
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151 :param g_name: List with Name of Genus for genomes from which the new marker has been extracted
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152 :param g_id: List with NCBI id of Genus for genomes from which the new marker has been extracted
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153 :param s_name: List with Name of Species for genomes from which the new marker has been extracted
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154 :param s_id: List with NCBI id of Species for genomes from which the new marker has been extracted
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155 :param t_name: List with Name of Strain for genomes from which the new marker has been extracted
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156 '''
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157 metadata = load_from_json(in_json_fp)
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158
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159 # check that all lists have same size
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160 genome_n = len(g_length)
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161 if len(gca) != genome_n:
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162 raise ValueError("Missing/Extra values in GCA list")
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163 if len(k_name) != genome_n:
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164 raise ValueError("Missing/Extra values in Kingdom name list")
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165 if len(k_id) != genome_n:
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166 raise ValueError("Missing/Extra values in Kingdom ID list")
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167 if len(p_name) != genome_n:
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168 raise ValueError("Missing/Extra values in Phylum name list")
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169 if len(p_id) != genome_n:
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170 raise ValueError("Missing/Extra values in Phylum ID list")
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171 if len(c_name) != genome_n:
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172 raise ValueError("Missing/Extra values in Class name list")
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173 if len(c_id) != genome_n:
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174 raise ValueError("Missing/Extra values in Class ID list")
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175 if len(o_name) != genome_n:
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176 raise ValueError("Missing/Extra values in Order name list")
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177 if len(o_id) != genome_n:
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178 raise ValueError("Missing/Extra values in Order ID list")
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179 if len(f_name) != genome_n:
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180 raise ValueError("Missing/Extra values in Family name list")
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181 if len(f_id) != genome_n:
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182 raise ValueError("Missing/Extra values in Family ID list")
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183 if len(g_name) != genome_n:
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184 raise ValueError("Missing/Extra values in Genus name list")
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185 if len(g_id) != genome_n:
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186 raise ValueError("Missing/Extra values in Genus ID list")
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187 if len(s_name) != genome_n:
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diff changeset
188 raise ValueError("Missing/Extra values in Species name list")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
189 if len(s_id) != genome_n:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
190 raise ValueError("Missing/Extra values in Species ID list")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
191 if len(t_name) != genome_n:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
192 raise ValueError("Missing/Extra values in Strain name list")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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diff changeset
193
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
194 # create dictionary to aggregate genome taxonomies and identify marker taxonomy
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
195 taxonomy = {
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
196 'k': set(),
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
197 'p': set(),
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
198 'c': set(),
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
199 'o': set(),
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
200 'f': set(),
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
201 'g': set(),
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
202 's': set(),
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
203 't': set(),
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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204 }
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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205
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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206 # parse genomes
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
207 for i in range(genome_n):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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208 # add taxonomy of new genome
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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209 g_taxo_names = "k__%s|p__%s|c__%s|o__%s|f__%s|g__%s|s__%s|t__%s" % (
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
210 k_name[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
211 p_name[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
212 c_name[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
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213 o_name[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
214 f_name[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
215 g_name[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
216 s_name[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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diff changeset
217 t_name[i]
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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218 )
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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219 g_taxo_ids = "%s|%s|%s|%s|%s|%s|%s" % (
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
220 k_id[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
221 p_id[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
222 c_id[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
223 o_id[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
224 f_id[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
225 g_id[i],
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
226 s_id[i]
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
227 )
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
228 metadata['taxonomy'][g_taxo_names] = (g_taxo_ids, g_length[i])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
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229 # aggregate taxon levels using sets
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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diff changeset
230 taxonomy['k'].add(k_name[i])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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231 taxonomy['p'].add(p_name[i])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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diff changeset
232 taxonomy['c'].add(c_name[i])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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233 taxonomy['o'].add(o_name[i])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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diff changeset
234 taxonomy['f'].add(f_name[i])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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diff changeset
235 taxonomy['g'].add(g_name[i])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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236 taxonomy['s'].add(s_name[i])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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237 taxonomy['t'].add(t_name[i])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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238
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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239 # extract clade and taxon of marker
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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240 clade = '' # last level before taxomy of genomes diverge
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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241 taxon = '' # combination of levels before divergence
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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242 for level in ['k', 'p', 'c', 'o', 'f', 'g', 's', 't']:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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243 taxo = list(taxonomy[level])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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244 if len(taxo) == 1:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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diff changeset
245 clade = taxo[0]
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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246 taxon = "%s|%s__%s" % (taxon, level, taxo)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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247
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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248 # add information about the new marker
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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249 metadata['markers'][name] = {
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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diff changeset
250 'clade': clade,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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251 'ext': set(gca),
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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252 'len': m_length,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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253 'taxon': taxon
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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254 }
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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255
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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256 dump_to_json(metadata, out_json_fp)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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257
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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258
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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259 def format_markers(marker_l):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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260 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
261 Format markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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262
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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diff changeset
263 :param marker_l: list of markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
264 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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diff changeset
265 markers = []
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
266 for m in marker_l:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
267 m = m.rstrip()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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diff changeset
268 if ' ' in m:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
269 markers.append(m.split(' ')[0])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
270 else:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
271 markers.append(m)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
272 return markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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diff changeset
273
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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274
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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275 def get_markers(marker_fp):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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276 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
277 Get markers from a file
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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278
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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279 :param marker_fp: Path to file with markers (1 per line)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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diff changeset
280 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
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281 # load markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
282 with open(marker_fp, 'r') as marker_f:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
283 markers = marker_f.readlines()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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284
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
285 # format markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
286 markers = format_markers(markers)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
287
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
288 return markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
289
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
290
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
291 def check_not_found_markers(found_markers, original_markers):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
292 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
293 Check list of markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
294
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
295 :param found_markers: list of found markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
296 :param original_markers: list of original markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
297 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
298 if len(found_markers) != len(original_markers):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
299 print('markers not found:')
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
300 for m in original_markers:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
301 if m not in found_markers:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
302 print('- "%s"' % m)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
303
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
304
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
305 def prune_taxonomy(in_taxonomy, taxon_s, gca_s):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
306 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
307 Prune taxonomy to keep only listed taxonomy
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
308
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
309 :param in_taxonomy: dictionary with list of taxonomy
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
310 :param taxon_s: set of taxons to keep
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
311 :param gca_s: set of GCA ids to keep
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
312 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
313 out_taxonomy = {}
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
314 kept_taxonomy = set()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
315 kept_taxons = set()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
316 kept_gca = set()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
317 for t, v in in_taxonomy.items():
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
318 # check if t match element in list of taxon_s
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
319 kept_taxon = False
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
320 for t_k in taxon_s:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
321 if t_k in t:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
322 kept_taxon = True
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
323 out_taxonomy[t] = v
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
324 kept_taxonomy.add(t)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
325 kept_taxons.add(t_k)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
326 break
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
327 # check if GCA in the taxon id
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
328 s = re.search(r'GCA_\d+$', t)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
329 if s:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
330 gca = s[0]
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
331 # check if GCA in taxon id is in the list GCA to keep
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
332 if gca in gca_s:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
333 kept_gca.add(gca)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
334 if not kept_taxon:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
335 out_taxonomy[t] = v
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
336 kept_taxonomy.add(t)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
337
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
338 print('%s kept taxonomy' % len(kept_taxonomy))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
339 print('%s / %s taxons not found' % (len(taxon_s) - len(kept_taxons), len(taxon_s)))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
340 print('%s / %s GCA taxons not found' % (len(gca_s) - len(kept_gca), len(gca_s)))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
341 return out_taxonomy
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
342
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
343
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
344 def remove_markers(in_json_fp, marker_fp, out_json_fp, kept_marker_fp):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
345 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
346 Remove markers from JSON file
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
347
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
348 :param in_json_fp: Path to input JSON file
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
349 :param marker_fp: Path to file with markers to remove (1 per line)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
350 :param out_json_fp: Path to output JSON file
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
351 :param kept_marker_fp: Path to file with kept markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
352 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
353 in_metadata = load_from_json(in_json_fp)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
354
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
355 # load markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
356 markers_to_remove = set(get_markers(marker_fp))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
357 print('%s markers to remove' % len(markers_to_remove))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
358
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
359 # keep merged_taxon
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
360 out_metadata = {
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
361 'markers': {},
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
362 'taxonomy': {},
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
363 'merged_taxon': in_metadata['merged_taxon']
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
364 }
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
365
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
366 # parse markers to keep
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
367 removed_markers = []
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
368 kept_markers = []
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
369 taxons_to_keep = set()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
370 gca_to_keep = set()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
371 for m, v in in_metadata['markers'].items():
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
372 if m not in markers_to_remove:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
373 out_metadata['markers'][m] = v
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
374 kept_markers.append(m)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
375 taxons_to_keep.add(v['taxon'])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
376 gca_to_keep.update(v['ext'])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
377 else:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
378 removed_markers.append(m)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
379 print('%s removed markers' % len(removed_markers))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
380
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
381 # check markers that are not found
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
382 check_not_found_markers(removed_markers, markers_to_remove)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
383
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
384 # keep only taxonomy in taxons_to_keep or with GCA in gca_to_keep
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
385 out_metadata['taxonomy'] = prune_taxonomy(in_metadata['taxonomy'], taxons_to_keep, gca_to_keep)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
386
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
387 # save to JSON
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
388 dump_to_json(out_metadata, out_json_fp)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
389
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
390 # write list of kept markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
391 with open(kept_marker_fp, 'w') as kept_marker_f:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
392 for m in kept_markers:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
393 kept_marker_f.write("%s\n" % m)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
394
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
395
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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diff changeset
396 def keep_markers(in_json_fp, marker_fp, out_json_fp):
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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parents:
diff changeset
397 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
398 Keep markers from JSON file, others will be removed
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
399
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
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diff changeset
400 :param in_json_fp: Path to input JSON file
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
401 :param marker_fp: Path to file with markers to keep (1 per line)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
402 :param out_json_fp: Path to output JSON file
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
403 '''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
404 in_metadata = load_from_json(in_json_fp)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
405
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
406 # load markers
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
407 markers_to_keep = set(get_markers(marker_fp))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
408 print('%s markers to keep' % len(markers_to_keep))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
409
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
410 # keep merged_taxon
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
411 out_metadata = {
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
412 'markers': {},
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
413 'taxonomy': {},
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
414 'merged_taxon': in_metadata['merged_taxon']
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
415 }
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
416
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
417 # parse markers to keep
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
418 kept_markers = []
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
419 taxons_to_keep = set()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
420 gca_to_keep = set()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
421 for m, v in in_metadata['markers'].items():
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
422 if m in markers_to_keep:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
423 out_metadata['markers'][m] = v
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
424 kept_markers.append(m)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
425 taxons_to_keep.add(v['taxon'])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
426 gca_to_keep.update(v['ext'])
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
427 print('%s kept markers' % len(kept_markers))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
428
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
429 # check markers that are not found
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
430 check_not_found_markers(kept_markers, markers_to_keep)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
431
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
432 # keep only taxonomy in taxons_to_keep or with GCA in gca_to_keep
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
433 out_metadata['taxonomy'] = prune_taxonomy(in_metadata['taxonomy'], taxons_to_keep, gca_to_keep)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
434
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
435 # save to JSON
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
436 dump_to_json(out_metadata, out_json_fp)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
437
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
438
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
439 if __name__ == '__main__':
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
440 # Read command line
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
441 parser = argparse.ArgumentParser(description='Customize MetaPhlan database')
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
442 subparsers = parser.add_subparsers(dest='function')
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
443 # transform_pkl_to_json subcommand
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
444 pkl_to_json_parser = subparsers.add_parser('transform_pkl_to_json', help='Transform Pickle to JSON to get marker metadata')
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
445 pkl_to_json_parser.add_argument('--pkl', help="Path to input Pickle file")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
446 pkl_to_json_parser.add_argument('--json', help="Path to output JSON file")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
447 # transform_json_to_pkl subcommand
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
448 json_to_pkl_parser = subparsers.add_parser('transform_json_to_pkl', help='Transform JSON to Pickle to push marker metadata')
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
449 json_to_pkl_parser.add_argument('--json', help="Path to input JSON file")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
450 json_to_pkl_parser.add_argument('--pkl', help="Path to output Pickle file")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
451 # add_marker subcommand
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
452 add_marker_parser = subparsers.add_parser('add_marker', help='Add new marker to JSON file')
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
453 add_marker_parser.add_argument('--in_json', help="Path to input JSON file")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
454 add_marker_parser.add_argument('--out_json', help="Path to output JSON file")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
455 add_marker_parser.add_argument('--name', help="Name of new marker")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
456 add_marker_parser.add_argument('--m_length', help="Length of new marker")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
457 add_marker_parser.add_argument('--g_length', help="Length of genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
458 add_marker_parser.add_argument('--gca', help="GCA of genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
459 add_marker_parser.add_argument('--k_name', help="Name of Kingdom for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
460 add_marker_parser.add_argument('--k_id', help="NCBI id of Kingdom for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
461 add_marker_parser.add_argument('--p_name', help="Name of Phylum for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
462 add_marker_parser.add_argument('--p_id', help="NCBI id of Phylum for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
463 add_marker_parser.add_argument('--c_name', help="Name of Class for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
464 add_marker_parser.add_argument('--c_id', help="NCBI id of Class for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
465 add_marker_parser.add_argument('--o_name', help="Name of Order for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
466 add_marker_parser.add_argument('--o_id', help="NCBI id of Order for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
467 add_marker_parser.add_argument('--f_name', help="Name of Family for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
468 add_marker_parser.add_argument('--f_id', help="NCBI id of Family for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
469 add_marker_parser.add_argument('--g_name', help="Name of Genus for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
470 add_marker_parser.add_argument('--g_id', help="NCBI id of Genus for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
471 add_marker_parser.add_argument('--s_name', help="Name of Species for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
472 add_marker_parser.add_argument('--s_id', help="NCBI id of Species for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
thanhlv
parents:
diff changeset
473 add_marker_parser.add_argument('--t_name', help="Name of Strain for genome from which the new marker has been extracted", action="append")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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474 # remove_markers subcommand
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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475 remove_markers_parser = subparsers.add_parser('remove_markers', help='Remove markers from JSON file')
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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476 remove_markers_parser.add_argument('--in_json', help="Path to input JSON file")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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477 remove_markers_parser.add_argument('--markers', help="Path to file with markers to remove (1 per line)")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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478 remove_markers_parser.add_argument('--out_json', help="Path to output JSON file")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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479 remove_markers_parser.add_argument('--kept_markers', help="Path to file with kept markers")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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480 # keep_markers subcommand
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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481 keep_markers_parser = subparsers.add_parser('keep_markers', help='Keep markers from JSON file, others will be removed')
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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482 keep_markers_parser.add_argument('--in_json', help="Path to input JSON file")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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483 keep_markers_parser.add_argument('--markers', help="Path to file with markers to keep (1 per line)")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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484 keep_markers_parser.add_argument('--out_json', help="Path to output JSON file")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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485
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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486 args = parser.parse_args()
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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487
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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488 if args.function == 'transform_pkl_to_json':
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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489 validate_map_version(Path(args.pkl), 'pkl')
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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490 transform_pkl_to_json(Path(args.pkl), Path(args.json))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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491 elif args.function == 'transform_json_to_pkl':
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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492 validate_map_version(Path(args.json), 'json')
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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493 transform_json_to_pkl(Path(args.json), Path(args.pkl))
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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494 elif args.function == 'add_marker':
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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495 add_marker(
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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496 args.in_json,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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497 args.out_json,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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498 args.name,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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499 args.m_length,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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500 args.g_length,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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501 args.gca,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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502 args.k_name,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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503 args.k_id,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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504 args.p_name,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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505 args.p_id,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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506 args.c_name,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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507 args.c_id,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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508 args.o_name,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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509 args.o_id,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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510 args.f_name,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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511 args.f_id,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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512 args.g_name,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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513 args.g_id,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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514 args.s_name,
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
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515 args.s_id,
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516 args.t_name)
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517 elif args.function == 'remove_markers':
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518 remove_markers(args.in_json, args.markers, args.out_json, args.kept_markers)
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519 elif args.function == 'keep_markers':
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520 keep_markers(args.in_json, args.markers, args.out_json)