Mercurial > repos > iuc > extract_metaphlan_database

annotate formatoutput.py @ 1:1aaa9b943a83 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
author iuc
date Mon, 17 May 2021 20:08:58 +0000
parents
children b6ecdfac241f
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1
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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diff changeset
1 #!/usr/bin/env python
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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2 # -*- coding: utf-8 -*-
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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3
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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4 import argparse
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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5 import re
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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6 from pathlib import Path
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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7
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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8 taxo_level = {
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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9 'k': 'kingdom',
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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10 'p': 'phylum',
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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11 'c': 'class',
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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12 'o': 'order',
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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13 'f': 'family',
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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14 'g': 'genus',
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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15 's': 'species',
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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16 't': 'strains'}
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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17
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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18
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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19 def split_levels(metaphlan_output_fp, out_dp, legacy_output):
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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20 '''
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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21 Split default MetaPhlAn into a report for each taxonomic level
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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22
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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23 :param metaphlan_output_fp: Path default MetaPhlAn output
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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24 :param out_dp: Path to output directory
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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25 :param legacy_output: Boolean for legacy output
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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26 '''
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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27 # prepare output files
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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28 abund_f = {
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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29 'k': open(out_dp / Path('kingdom'), 'w'),
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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30 'p': open(out_dp / Path('phylum'), 'w'),
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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31 'c': open(out_dp / Path('class'), 'w'),
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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32 'o': open(out_dp / Path('order'), 'w'),
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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33 'f': open(out_dp / Path('family'), 'w'),
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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34 'g': open(out_dp / Path('genus'), 'w'),
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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35 's': open(out_dp / Path('species'), 'w'),
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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36 't': open(out_dp / Path('strains'), 'w')
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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37 }
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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38 for level in abund_f:
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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39 abund_f[level].write("%s\t" % taxo_level[level])
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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40 if not legacy_output:
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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41 abund_f[level].write("%s_id\t" % taxo_level[level])
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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42 abund_f[level].write("abundance\n")
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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43
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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44 levels_number = len(taxo_level)
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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45
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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46 with open(metaphlan_output_fp, 'r') as metaphlan_output_f:
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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47 with open(out_dp / Path('all'), 'w') as all_level_f:
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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48 # write header in all leve file
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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49 for level in ['k', 'p', 'c', 'o', 'f', 'g', 's', 't']:
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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50 all_level_f.write("%s\t" % taxo_level[level])
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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51 if not legacy_output:
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52 all_level_f.write("%s_id\t" % taxo_level[level])
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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53 all_level_f.write("abundance\n")
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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54
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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55 # parse metaphlan file
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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56 for line in metaphlan_output_f.readlines():
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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57 # skip headers
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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58 if line.startswith("#"):
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59 continue
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60
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61 # spit lines
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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62 split_line = line[:-1].split('\t')
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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63 taxo_n = split_line[0].split('|')
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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64 if legacy_output:
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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65 abundance = split_line[1]
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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66 else:
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67 taxo_id = split_line[1].split('|')
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68 abundance = split_line[2]
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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69
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70 # get taxon name and ids
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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71 for i in range(len(taxo_n)):
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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72 taxo = taxo_n[i].split('__')[1]
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73 taxo = taxo.replace("_", " ")
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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74 all_level_f.write("%s\t" % taxo)
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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75 if not legacy_output:
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76 all_level_f.write("%s\t" % taxo_id[i])
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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77
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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78 # if not all taxon levels
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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79 for i in range(len(taxo_n), levels_number):
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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80 all_level_f.write('\t')
1aaa9b943a83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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81
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82 all_level_f.write("%s\n" % abundance)
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83
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84 # write
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85 last_taxo_level = taxo_n[-1].split('__')
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86 taxo = last_taxo_level[1].replace("_", " ")
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87 level = last_taxo_level[0]
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88 abund_f[level].write("%s\t" % taxo)
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89 if not legacy_output:
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90 abund_f[level].write("%s\t" % taxo_id[-1])
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91 abund_f[level].write("%s\n" % abundance)
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92
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93 # close files
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94 for taxo_level_f in abund_f:
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95 abund_f[taxo_level_f].close()
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96
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97
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98 def format_for_krona(metaphlan_output_fp, krona_out_fp):
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99 '''
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100 Split default MetaPhlAn into a report for each taxonomic levKRONAel
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101
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102 :param metaphlan_output_fp: Path default MetaPhlAn output
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103 :param krona_out: Path to output file for Krona
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104 '''
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105 re_replace = re.compile(r"\w__")
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106 re_bar = re.compile(r"\|")
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107 re_underscore = re.compile(r"_")
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108
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109 with open(metaphlan_output_fp, 'r') as metaphlan_output_f:
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110 with open(krona_out_fp, 'w') as krona_out_f:
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111 for line in metaphlan_output_f.readlines():
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112 if "s__" in line:
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113 x = line.rstrip().split('\t')
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114 lineage = re.sub(re_bar, '', x[0])
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115 lineage = re.sub(re_replace, '\t', lineage)
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116 lineage = re.sub(re_underscore, ' ', lineage)
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117 krona_out_f.write("%s\t%s\n" % (x[-1], lineage))
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118
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119
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120 if __name__ == '__main__':
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121 parser = argparse.ArgumentParser(description='Format MetaPhlAn output')
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122 subparsers = parser.add_subparsers(dest='function')
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123 # split_levels
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124 split_levels_parser = subparsers.add_parser('split_levels', help='Split default MetaPhlAn into a report for each taxonomic level')
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125 split_levels_parser.add_argument('--metaphlan_output', help="Path to default MetaPhlAn output")
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126 split_levels_parser.add_argument('--outdir', help="Path to output directory")
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127 split_levels_parser.add_argument('--legacy-output', dest='legacy_output', action='store_true', help="Old MetaPhlAn2 two columns output")
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128 split_levels_parser.set_defaults(legacy_output=False)
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129 # format_for_krona
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130 format_for_krona_parser = subparsers.add_parser('format_for_krona', help='Split default MetaPhlAn into a report for each taxonomic level')
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131 format_for_krona_parser.add_argument('--metaphlan_output', help="Path to default MetaPhlAn output")
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132 format_for_krona_parser.add_argument('--krona_output', help="Path to Krona output directory")
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133
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134 args = parser.parse_args()
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135
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136 if args.function == 'split_levels':
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137 split_levels(
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138 Path(args.metaphlan_output),
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139 Path(args.outdir),
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140 args.legacy_output)
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141 elif args.function == 'format_for_krona':
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142 format_for_krona(
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143 Path(args.metaphlan_output),
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144 Path(args.krona_output))