Mercurial > repos > bebatut > format_metaphlan2_output

annotate format_metaphlan2_output.py @ 0:aa68d226892e draft default tip

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
author bebatut
date Wed, 20 Apr 2016 07:52:22 -0400
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aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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1 #!/usr/bin/env python
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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2 # -*- coding: utf-8 -*-
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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4 import sys
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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5 import os
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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6 import argparse
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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7 import re
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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9 taxo_level_correspondance = {}
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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10 taxo_level_correspondance['k'] = 'kingdom'
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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11 taxo_level_correspondance['p'] = 'phylum'
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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12 taxo_level_correspondance['c'] = 'class'
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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13 taxo_level_correspondance['o'] = 'order'
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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14 taxo_level_correspondance['f'] = 'family'
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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15 taxo_level_correspondance['g'] = 'genus'
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16 taxo_level_correspondance['s'] = 'species'
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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17 taxo_level_correspondance['t'] = 'strains'
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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19 def write_taxo_abundance(output_files, level, taxo, abundance):
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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20 if not taxo_level_correspondance.has_key(level):
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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21 raise ValueError(level + ' is not a know taxonomic level')
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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22 output_files[taxo_level_correspondance[level]].write(taxo + '\t')
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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23 output_files[taxo_level_correspondance[level]].write(abundance + '\n')
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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25 def format_metaphlan2_output(args):
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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26 taxo_levels_abundance_files = {}
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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27 taxo_levels_abundance_files['kingdom'] = open(args.kingdom_abundance_file, 'w')
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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28 taxo_levels_abundance_files['phylum'] = open(args.phylum_abundance_file, 'w')
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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29 taxo_levels_abundance_files['class'] = open(args.class_abundance_file, 'w')
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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30 taxo_levels_abundance_files['order'] = open(args.order_abundance_file, 'w')
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31 taxo_levels_abundance_files['family'] = open(args.family_abundance_file, 'w')
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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32 taxo_levels_abundance_files['genus'] = open(args.genus_abundance_file, 'w')
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33 taxo_levels_abundance_files['species'] = open(args.species_abundance_file, 'w')
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34 taxo_levels_abundance_files['strains'] = open(args.strains_abundance_file, 'w')
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35
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36 for taxo_level_file in taxo_levels_abundance_files:
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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37 taxo_levels_abundance_files[taxo_level_file].write(taxo_level_file + '\t')
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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38 taxo_levels_abundance_files[taxo_level_file].write('abundance\n')
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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39
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40 with open(args.metaphlan2_output, 'r') as input_file:
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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41 with open(args.all_taxo_level_abundance_file, 'w') as output_file:
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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42 output_file.write("kingdom\t")
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43 output_file.write("phylum\t")
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44 output_file.write("class\t")
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45 output_file.write("order\t")
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46 output_file.write("family\t")
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47 output_file.write("genus\t")
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48 output_file.write("species\t")
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49 output_file.write("strains\t")
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50 output_file.write("abundance\n")
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51 levels_number = 8
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52
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53 for line in input_file.readlines():
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54 if line.startswith("#"):
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55 continue
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57 split_line = line[:-1].split('\t')
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58 all_taxo = split_line[0]
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59 abundance = split_line[1]
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60
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61 split_taxo = all_taxo.split('|')
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62 for level in split_taxo:
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63 taxo = level.split('__')[1]
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64 taxo = taxo.replace("_"," ")
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65 output_file.write(taxo + '\t')
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66
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67 for i in range(len(split_taxo), levels_number):
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68 output_file.write('\t')
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70 output_file.write(abundance + "\n")
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72
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73 last_taxo_level = split_taxo[-1].split('__')
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74 taxo = last_taxo_level[1].replace("_"," ")
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75 level = last_taxo_level[0]
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76 write_taxo_abundance(taxo_levels_abundance_files, level, taxo,
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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77 abundance)
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78
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79 for taxo_level_file in taxo_levels_abundance_files:
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80 taxo_levels_abundance_files[taxo_level_file].close()
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81
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82 if __name__ == '__main__':
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83 parser = argparse.ArgumentParser()
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84 parser.add_argument('--metaphlan2_output', required=True)
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85 parser.add_argument('--all_taxo_level_abundance_file', required=True)
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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86 parser.add_argument('--kingdom_abundance_file', required=True)
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87 parser.add_argument('--phylum_abundance_file', required=True)
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88 parser.add_argument('--class_abundance_file', required=True)
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89 parser.add_argument('--order_abundance_file', required=True)
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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90 parser.add_argument('--family_abundance_file', required=True)
aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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91 parser.add_argument('--genus_abundance_file', required=True)
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92 parser.add_argument('--species_abundance_file', required=True)
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93 parser.add_argument('--strains_abundance_file', required=True)
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94
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95 args = parser.parse_args()
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96
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97 format_metaphlan2_output(args)