Mercurial > repos > earlhaminst > ete

annotate ete_lineage_generator.py @ 12:dc32007a6b36 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit c568584f1eaa1366603b89db7e52994812f5d387
author earlhaminst
date Tue, 07 Jun 2022 08:58:05 +0000
parents 2db72467da51
children
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03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
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1 import optparse
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
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2 import sys
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3
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earlhaminst
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4 from ete3 import NCBITaxa
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5
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earlhaminst
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6 # - compared to gi2taxonomy the root is excluded, since
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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7 # the value is always "root", i.e. useless information
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8 # - additional levels that appear in the ncbi taxdb have
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earlhaminst
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9 # been added
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10 # (order from https://en.wikipedia.org/wiki/Taxonomic_rank#All_ranks)
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11 # TODO the full list of ranks could be derived from the input DB
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12 LONG_RANKS = [u"superkingdom", u"kingdom", u"subkingdom",
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13 u"superphylum", u"phylum", u"subphylum",
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14 u"superclass", u"class", u"subclass", "infraclass",
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15 u"cohort",
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16 u"superorder", u"order", u"suborder", u"infraorder", u"parvorder",
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17 u"superfamily", u"family", u"subfamily",
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18 u"tribe", u"subtribe",
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19 u"genus", u"subgenus",
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20 u"species group", u"species subgroup", u"species", u"subspecies",
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21 u"varietas", "forma"]
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22
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23 SHORT_RANKS = [u"kingdom",
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24 u"phylum",
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25 u"class",
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26 u"order",
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27 u"family",
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28 u"genus",
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29 u"species"]
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30
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31
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32 def process_taxid(ncbi, taxid, ranks, RANK_IDX, lower=False):
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33 """
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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34 process one taxid:
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35 - get lineage (as list of taxids, ranks, and names)
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36 - reverse the lineage if lower ranks are to be used for filling
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earlhaminst
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37 - fill the ranks with the data from the lineage
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
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38 ncbi: ete NCBITaxa object
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39 taxid: a taxid (int)
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40 ranks: list of ranks (should be initialized with "NA" x number of levels of interest)
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41 RANK_IDX: mapping from rank names to indices (distance to root/leaf?)
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42 lower: use lower taxa for filling "NA"s
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43 """
11
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44 try:
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45 lineage_taxids = ncbi.get_lineage(taxid)
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46 except ValueError:
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47 sys.stderr.write("[%s] could not determine lineage!\n" % taxid)
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earlhaminst
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48 return
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49 if lineage_taxids is None:
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50 sys.stderr.write("[%s] could not determine lineage!\n" % taxid)
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51 return
9
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52 lineage_ranks = ncbi.get_rank(lineage_taxids)
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53 lineage_names = ncbi.get_taxid_translator(lineage_taxids, try_synonyms=True)
2
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54 if lower:
9
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55 lineage_taxids.reverse()
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56 for parent_taxid in lineage_taxids:
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57 parent_rank = lineage_ranks[parent_taxid]
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58 if parent_rank not in RANK_IDX:
2
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59 continue
9
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60 parent_rank_index = RANK_IDX[parent_rank]
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61 if ranks[parent_rank_index] != "NA":
2
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62 continue
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63 ranks[parent_rank_index] = lineage_names[parent_taxid]
2
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64
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65
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66 # get command line options
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67 parser = optparse.OptionParser()
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68 parser.add_option('-s', '--species', dest="input_species_filename",
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69 help='Species/taxid list in text format one species in each line')
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70 parser.add_option('-d', '--database', dest="database", default=None,
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71 help='ETE sqlite data base to use (default: ~/.etetoolkit/taxa.sqlite)')
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72 parser.add_option('-o', '--output', dest="output", help='output file name (default: stdout)')
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73 parser.add_option('-f', dest="full", action="store_true", default=False,
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74 help='Show all available (named) taxonomic ranks (default: only primary levels)')
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75 parser.add_option('-c', dest="compress", action="store_true", default=False,
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76 help='Fill unnamed ranks with super/sub ranks (see -l)')
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77 parser.add_option('-l', dest="lower", action="store_true", default=False,
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78 help='Prefer lower levels when compressed')
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79 parser.add_option('-r', '--rank', dest='ranks', action="append",
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80 help='include rank - multiple ones can be specified')
6
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81 parser.add_option('-i', '--includeid', dest="addid", action="store_true", default=False,
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82 help='add taxid column')
2
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83
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84 options, args = parser.parse_args()
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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85 # check command line options
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earlhaminst
parents:
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86 if options.input_species_filename is None:
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earlhaminst
parents:
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87 parser.error("-s option must be specified, Species list in text format one species in each line")
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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88 if options.full and options.ranks:
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earlhaminst
parents:
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89 parser.error("-f and -r can not be used at the same time")
4
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earlhaminst
parents: 2
diff changeset
90
2
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earlhaminst
parents:
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91 if options.ranks:
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earlhaminst
parents:
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92 for r in options.ranks:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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93 if r not in LONG_RANKS:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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94 parser.error("unknown rank %s" % r)
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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95 # setup output
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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96 if not options.output: # if filename is not given
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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97 of = sys.stdout
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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98 else:
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earlhaminst
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99 of = open(options.output, "w")
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earlhaminst
parents:
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100 # load NCBI taxonomy DB
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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101 ncbi = NCBITaxa(dbfile=options.database)
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earlhaminst
parents:
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102 # get list of ranks that are of interest
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earlhaminst
parents:
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103 if options.ranks:
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earlhaminst
parents:
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104 RANKS = []
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earlhaminst
parents:
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105 for r in LONG_RANKS:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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106 if r in options.ranks:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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107 RANKS.append(r)
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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108 else:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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109 if options.full:
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earlhaminst
parents:
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110 RANKS = LONG_RANKS
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earlhaminst
parents:
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111 else:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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112 RANKS = SHORT_RANKS
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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113 RANK_IDX = {item: index for index, item in enumerate(RANKS)}
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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114 COMP_RANK_IDX = RANK_IDX
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earlhaminst
parents:
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115 if options.compress:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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116 for ir in range(len(RANKS)):
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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117 for ilr in range(len(LONG_RANKS)):
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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118 if RANKS[ir] in LONG_RANKS[ilr]:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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parents:
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119 COMP_RANK_IDX[LONG_RANKS[ilr]] = ir
6
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diff changeset
120
4
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earlhaminst
parents: 2
diff changeset
121 # write header
6
f1eca1158f21 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73
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122 of.write("# query")
f1eca1158f21 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73
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diff changeset
123 if options.addid:
f1eca1158f21 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73
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124 of.write("\ttaxid")
f1eca1158f21 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73
earlhaminst
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125 of.write("\t%s\n" % ("\t".join(RANKS)))
f1eca1158f21 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73
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diff changeset
126
4
87b6de3ef63e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 41e40314a9b25a9f3c06a13422d367b68334f593
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127 # get and write data
2
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128 with open(options.input_species_filename) as f:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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129 for line in f.readlines():
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130 line = line.strip().replace('_', ' ')
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2db72467da51 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 67e136d433c0d925db362342919305b46fdffecd"
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131 if line == "":
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earlhaminst
parents: 9
diff changeset
132 continue
2
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earlhaminst
parents:
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133 try:
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earlhaminst
parents:
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134 taxid = int(line)
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earlhaminst
parents:
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135 except ValueError:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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136 # TODO: one could use fuzzy name lookup (i.e. accept typos in the species names),
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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137 # but then a pysqlite version that supports this is needed (needs to be enabled
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earlhaminst
parents:
diff changeset
138 # during compilation)
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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139 name2tax = ncbi.get_name_translator([line])
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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140 if line in name2tax:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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141 taxid = name2tax[line][0]
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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parents:
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142 else:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
diff changeset
143 sys.stderr.write("[%s] could not be translated into a taxid!\n" % line)
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
diff changeset
144 continue
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
diff changeset
145 ranks = ["NA"] * len(RANKS)
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
diff changeset
146 process_taxid(ncbi, taxid, ranks, RANK_IDX)
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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147 if options.compress:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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148 process_taxid(ncbi, taxid, ranks, COMP_RANK_IDX, options.lower)
6
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earlhaminst
parents: 4
diff changeset
149 of.write("%s" % line)
f1eca1158f21 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73
earlhaminst
parents: 4
diff changeset
150 if options.addid:
f1eca1158f21 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73
earlhaminst
parents: 4
diff changeset
151 of.write("\t%d" % taxid)
f1eca1158f21 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73
earlhaminst
parents: 4
diff changeset
152 of.write("\t%s\n" % "\t".join(ranks))
2
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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153 of.close()