Mercurial > repos > bebatut > combine_metaphlan2_humann2

annotate combine_metaphlan2_humann2.py @ 0:31394a0c0242 draft

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
author bebatut
date Fri, 15 Apr 2016 09:15:21 -0400
parents
children e25efca0a49c
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31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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1 #!/usr/bin/env python
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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2 # -*- coding: utf-8 -*-
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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3
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4 import sys
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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5 import os
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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6 import argparse
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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7 import re
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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8
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9 def extract_clade_abundance(metaphlan2_filepath):
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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10 clade_abundance = {}
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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11 with open(metaphlan2_filepath, 'r') as metaphlan2_file:
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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12 for line in metaphlan2_file.readlines():
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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13 if line.find('g__') == -1:
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14 continue
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16 split_line = line[:-1].split('\t')
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17 taxo = split_line[0]
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18 abundance = split_line[1]
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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19
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20 genus = taxo[(taxo.find('g__')+3):]
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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21 if genus.find('|') != -1:
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22 genus = genus[:(genus.find('|'))]
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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23 clade_abundance.setdefault(genus, {'abundance':0, 'species':{}})
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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24 if taxo.find('t__') != -1:
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25 continue
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26 elif taxo.find('s__') != -1:
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27 species = taxo[(taxo.find('s__')+3):]
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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28 clade_abundance[genus]['species'].setdefault(species, abundance)
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29 else:
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30 clade_abundance[genus]['abundance'] = abundance
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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31 return clade_abundance
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32
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33 def compute_overall_abundance(humann2_file):
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34 overall_abundance = 0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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35 with open(args.humann2_file, 'r') as humann2_file:
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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36 for line in humann2_file.readlines():
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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37 if line.find('|') != -1 or line.startswith('#'):
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38 continue
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39 split_line = line[:-1].split('\t')
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40 overall_abundance += float(split_line[1])
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41 return overall_abundance
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42
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43 def format_characteristic_name(name):
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44 formatted_name = name
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45 formatted_name = formatted_name.replace('/',' ')
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46 formatted_name = formatted_name.replace('-',' ')
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47 formatted_name = formatted_name.replace("'",'')
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48 if formatted_name.find('(') != -1 and formatted_name.find(')') != -1:
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49 open_bracket = formatted_name.find('(')
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50 close_bracket = formatted_name.find(')')+1
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51 formatted_name = formatted_name[:open_bracket] + formatted_name[close_bracket:]
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52 return formatted_name
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53
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54 def combine_metaphlan2_humann2(args):
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55 clade_abundance = extract_clade_abundance(args.metaphlan2_file)
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56 overall_abundance = compute_overall_abundance(args.humann2_file)
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57
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58 with open(args.output_file, 'w') as output_file:
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59 output_file.write('genus\t')
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60 output_file.write('genus_abundance\t')
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61 output_file.write('species\t')
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62 output_file.write('species_abundance\t')
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63 output_file.write(args.type + '_id\t')
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64 output_file.write(args.type + '_name\t')
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65 output_file.write(args.type + '_abundance\n')
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66 with open(args.humann2_file, 'r') as humann2_file:
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67 for line in humann2_file.readlines():
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68 if line.find('|') == -1:
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69 continue
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70
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71 split_line = line[:-1].split('\t')
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72 abundance = 100*float(split_line[1])/overall_abundance
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73 annotation = split_line[0].split('|')
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74 characteristic = annotation[0].split(':')
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75 characteristic_id = characteristic[0]
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76 characteristic_name = ''
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77 if len(characteristic) > 1:
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78 characteristic_name = format_characteristic_name(characteristic[-1])
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79 taxo = annotation[1].split('.')
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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80
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81 if taxo[0] == 'unclassified':
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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82 continue
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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83 genus = taxo[0][3:]
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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84 species = taxo[1][3:]
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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85
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86 if not clade_abundance.has_key(genus):
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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87 print "no", genus, "found in", args.metaphlan2_file
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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88 continue
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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89 if not clade_abundance[genus]['species'].has_key(species):
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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90 print "no", species, "found in", args.metaphlan2_file,
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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91 print "for", genus
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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92 continue
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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93 output_file.write(genus + '\t')
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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94 output_file.write(clade_abundance[genus]['abundance'] + '\t')
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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95 output_file.write(species + '\t')
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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96 output_file.write(clade_abundance[genus]['species'][species] + '\t')
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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97 output_file.write(characteristic_id + '\t')
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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98 output_file.write(characteristic_name + '\t')
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99 output_file.write(str(abundance) + '\n')
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100
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101 if __name__ == '__main__':
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102 parser = argparse.ArgumentParser()
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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103 parser.add_argument('--humann2_file', required=True)
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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104 parser.add_argument('--metaphlan2_file', required=True)
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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105 parser.add_argument('--output_file', required=True)
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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106 parser.add_argument('--type', required=True,
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107 choices = ['gene_families','pathways'])
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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108 args = parser.parse_args()
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
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109
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110 combine_metaphlan2_humann2(args)