Mercurial > repos > bebatut > compare_humann2_output

annotate compare_humann2_output.py @ 0:9959fa526f1a draft

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
author bebatut
date Wed, 20 Apr 2016 08:30:08 -0400
parents
children 05766022dfc4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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1 #!/usr/bin/env python
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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2 # -*- coding: utf-8 -*-
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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3
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4 import sys
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5 import os
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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6 import argparse
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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7 import re
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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8
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9 def extract_abundances(filepath, nb_charact_to_extract):
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10 abundances = {}
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11 more_abund_charact = []
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12 abund_sum = 0
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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13 with open(filepath, 'r') as abundance_file:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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14 for line in abundance_file.readlines()[1:]:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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15 split_line = line[:-1].split('\t')
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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16 charact_id = split_line[0]
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17 abund = float(split_line[1])
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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18 abundances[charact_id] = 100*abund
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19 abund_sum += abundances[charact_id]
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20
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21 if len(more_abund_charact) < nb_charact_to_extract:
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22 more_abund_charact.append(charact_id)
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23 else:
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24 best_pos = None
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25 for i in range(len(more_abund_charact)-1,-1,-1):
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26 if abundances[more_abund_charact[i]] < abund:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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27 best_pos = i
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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28 else:
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29 break
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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30 if best_pos != None:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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31 tmp_more_abund_charact = more_abund_charact
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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32 more_abund_charact = tmp_more_abund_charact[:best_pos]
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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33 more_abund_charact += [charact_id]
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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34 more_abund_charact += tmp_more_abund_charact[best_pos:-1]
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35 return abundances, more_abund_charact
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36
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37 def format_characteristic_name(all_name):
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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38 if all_name.find(':') != -1:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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39 charact_id = all_name.split(':')[0]
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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40 charact_name = all_name.split(':')[1][1:]
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41 else:
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42 charact_id = all_name
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43 charact_name = ''
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44
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45 charact_name = charact_name.replace('/',' ')
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46 charact_name = charact_name.replace('-',' ')
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47 charact_name = charact_name.replace("'",'')
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48 if charact_name.find('(') != -1 and charact_name.find(')') != -1:
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49 open_bracket = charact_name.find('(')
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50 close_bracket = charact_name.find(')')+1
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51 charact_name = charact_name[:open_bracket] + charact_name[close_bracket:]
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52 return charact_id,charact_name
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53
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54 def write_more_abundant_charat(abundances,more_abund_charact, output_filepath):
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55 with open(output_filepath,'w') as output_file:
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56 output_file.write('id\tname\t')
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57 output_file.write('\t'.join(abundances.keys()) + '\n')
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58
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59 for mac in more_abund_charact:
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60 charact_id,charact_name = format_characteristic_name(mac)
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61 output_file.write(charact_id + '\t' + charact_name)
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62 for sample in abundances:
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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63 abund = abundances[sample].get(mac, 0)
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64 output_file.write('\t' + str(abund))
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65 output_file.write('\n')
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66
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67 def extract_similar_characteristics(abundances, sim_output_filepath,
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68 specific_output_files):
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69 sim_characteristics = set(abundances[abundances.keys()[0]].keys())
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70 for sample in abundances.keys()[1:]:
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71 sim_characteristics.intersection_update(abundances[sample].keys())
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72 print 'Similar between all samples:', len(sim_characteristics)
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73
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74 with open(sim_output_filepath, 'w') as sim_output_file:
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75 sim_output_file.write('id\tname\t' + '\t'.join(abundances.keys()) + '\n')
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76 for charact in list(sim_characteristics):
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77 charact_id,charact_name = format_characteristic_name(charact)
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78 sim_output_file.write(charact_id + '\t' + charact_name)
9959fa526f1a planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
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79 for sample in abundances.keys():
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80 sim_output_file.write('\t' + str(abundances[sample][charact]))
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81 sim_output_file.write('\n')
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82
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83 print 'Specific to samples:'
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84 diff_characteristics = {}
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85 for i in range(len(abundances.keys())):
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86 sample = abundances.keys()[i]
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87 print ' ', sample, ""
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88 print ' All:', len(abundances[sample].keys())
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89 diff_characteristics[sample] = set(abundances[sample].keys())
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90 diff_characteristics[sample].difference_update(sim_characteristics)
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91 print ' Number of specific characteristics:',
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92 print len(diff_characteristics[sample])
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93 print ' Percentage of specific characteristics:',
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94 print 100*len(diff_characteristics[sample])/(1.*len(abundances[sample].keys()))
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95
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96 relative_abundance = 0
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97 with open(specific_output_files[i], 'w') as output_file:
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98 output_file.write('id\tname\tabundances\n')
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99 for charact in list(diff_characteristics[sample]):
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100 charact_id,charact_name = format_characteristic_name(charact)
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101 output_file.write(charact_id + '\t' + charact_name + '\t')
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102 output_file.write(str(abundances[sample][charact]) + '\n')
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103 relative_abundance += abundances[sample][charact]
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104 print ' Relative abundance of specific characteristics(%):', relative_abundance
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105
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106 return sim_characteristics
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107
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108 def compare_humann2_output(args):
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109 abundances = {}
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110 more_abund_charact = []
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111
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112 for i in range(len(args.sample_name)):
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113 abundances[args.sample_name[i]], mac = extract_abundances(args.charact_input_file[i],
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114 args.most_abundant_characteristics_to_extract)
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115 more_abund_charact += mac
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116
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117 write_more_abundant_charat(abundances, list(set(more_abund_charact)),
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118 args.more_abundant_output_file)
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119 sim_characteristics = extract_similar_characteristics(abundances,
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120 args.similar_output_file, args.specific_output_file)
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121
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122 if __name__ == '__main__':
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123 parser = argparse.ArgumentParser()
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124 parser.add_argument('--sample_name', required=True, action='append')
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125 parser.add_argument('--charact_input_file', required=True, action='append')
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126 parser.add_argument('--most_abundant_characteristics_to_extract', required=True,
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127 type = int)
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128 parser.add_argument('--more_abundant_output_file', required=True)
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129 parser.add_argument('--similar_output_file', required=True)
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130 parser.add_argument('--specific_output_file', required=True,action='append')
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131 args = parser.parse_args()
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132
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133 if len(args.sample_name) != len(args.charact_input_file):
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134 raise ValueError("Same number of values (in same order) are expected for --sample_name and --charact_input_file")
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135 if len(args.sample_name) != len(args.specific_output_file):
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136 raise ValueError("Same number of values (in same order) are expected for --sample_name and --specific_output_file")
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137
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138 compare_humann2_output(args)