Mercurial > repos > matthias > data_manager_dada2

annotate data_manager/data_manager.py @ 1:1c50cfb0c0ab draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
author matthias
date Thu, 07 Mar 2019 11:48:18 -0500
parents 419037fe1150
children b4c303665291
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419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
matthias
parents:
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1 import argparse
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
matthias
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2 import json
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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3 import os
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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4 import shutil
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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5 import sys
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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6 import zipfile
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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7 try:
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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8 # For Python 3.0 and later
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
matthias
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9 from urllib.request import Request, urlopen
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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10 except ImportError:
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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11 # Fall back to Python 2 imports
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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12 from urllib2 import Request, urlopen
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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13
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14 DEFAULT_TAXLEVELS="Kingdom,Phylum,Class,Order,Family,Genus,Species"
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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16 FILE2NAME = {
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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17 "silva132":"Silva version 132",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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18 "silva128":"Silva version 128",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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19 "rdp16":"RDP trainset 16",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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20 "rdp14":"RDP trainset 14",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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21 "gg13.84":"GreenGenes version 13.8",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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22 }
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24 FILE2TAXURL = {
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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25 "silva132":"https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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26 "silva128":"https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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27 "rdp16":"https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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28 "rdp14":"https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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29 "gg13.84":"https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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30 }
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32 FILE2SPECIESURL = {
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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33 "silva132":"https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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34 "silva128":"https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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35 "rdp16":"https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1",
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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36 "rdp14":"https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1"
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37 }
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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38
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39 FILE2TAXLEVELS = {
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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40 }
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41
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42 def url_download(url, fname, workdir):
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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43 """
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44 download url to workdir/fname
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45
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46 return the path to the resulting file
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47 """
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48 file_path = os.path.join(workdir, fname)
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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49 if not os.path.exists(workdir):
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50 os.makedirs(workdir)
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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51 src = None
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52 dst = None
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53 try:
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54 req = Request(url)
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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55 src = urlopen(req)
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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56 with open(file_path, 'wb') as dst:
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57 while True:
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58 chunk = src.read(2**10)
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59 if chunk:
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60 dst.write(chunk)
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61 else:
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62 break
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63 finally:
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64 if src:
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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65 src.close()
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66 return os.path.join(workdir, fname)
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67
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68 def main(dataset, outjson):
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69
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70 params = json.loads(open(outjson).read())
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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71 target_directory = params['output_data'][0]['extra_files_path']
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72 os.mkdir(target_directory)
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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73 output_path = os.path.abspath(os.path.join(os.getcwd(), 'dada2'))
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74
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75 workdir = os.path.join(os.getcwd(), 'dada2')
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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76 path = url_download( FILE2TAXURL[dataset], taxdataset+".taxonomy", workdir)
419037fe1150 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
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77
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78 data_manager_json = {"data_tables":{}}
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79 data_manager_entry = {}
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80 data_manager_entry['value'] = dataset
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81 data_manager_entry['name'] = FILE2NAME[dataset]
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82 data_manager_entry['path'] = path
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83 data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS)
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84 data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry
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87 if FILE2SPECIES.get(dataset, False ):
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88 path = url_download( FILE2SPECIES[dataset], taxdataset+".species", workdir)
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90 data_manager_entry = {}
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91 data_manager_entry['value'] = dataset
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92 data_manager_entry['name'] = FILE2NAME[dataset]
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93 data_manager_entry['path'] = path
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94 data_manager_json["data_tables"]["dada2_species"] = data_manager_entry
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96 for filename in os.listdir(workdir):
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97 shutil.move(os.path.join(output_path, filename), target_directory)
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98 file(outjson, 'w').write(json.dumps(data_manager_json))
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100 if __name__ == '__main__':
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101 parser = argparse.ArgumentParser(description='Create data manager json.')
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102 parser.add_argument('--out', action='store', help='JSON filename')
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103 parser.add_argument('--dataset', action='store', help='Download data set name')
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104 args = parser.parse_args()
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105
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106 main(args.dataset, args.out)