Mercurial > repos > matthias > data_manager_dada2

annotate data_manager/data_manager.py @ 2:b4c303665291 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 eec95ccc2189355061112ea2785b82f13a0fa077-dirty
author matthias
date Fri, 08 Mar 2019 05:38:44 -0500
parents 419037fe1150
children 3a4ee8bf012a
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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
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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
matthias
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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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14 DEFAULT_TAXLEVELS="Kingdom,Phylum,Class,Order,Family,Genus,Species"
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16 FILE2NAME = {
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17 "silva132":"Silva version 132",
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18 "silva128":"Silva version 128",
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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",
2
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matthias
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22 "unite8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
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23 "unite8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
matthias
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24 "unite8.0_euka": "UNITE: General Fasta release 8.0 for all Eukaryotes",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
matthias
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25 "unite8.0_euka_singletons": "UNITE: General Fasta release 8.0 for all Eukaryotes including global and 97% singletons",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
matthias
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26 "RefSeq_RDP_2018_05": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
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27 "gtdb_2018_11_20": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
matthias
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28 "hitdb1": "HitDB version 1 (Human InTestinal 16S rRNA)",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
matthias
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29 "silva132_euk_18S": "Silva version 132 Eukaryotic 18S",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
matthias
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30 "PR2v4.11.1": "Protist Ribosomal Reference database (PR2) 4.11.1"
0
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31 }
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32
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33 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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34 "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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35 "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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36 "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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37 "rdp14":"https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1",
2
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matthias
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38 "unite8.0_fungi": "https://files.plutof.ut.ee/public/orig/EB/0C/EB0CCB3A871B77EA75E472D13926271076904A588D2E1C1EA5AFCF7397D48378.zip",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
matthias
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39 "unite8.0_fungi_singletons": "https://files.plutof.ut.ee/doi/06/A2/06A2C86256EED64085670EB0C54B7115F6DAC8F311C656A9CB33E386CFABA0D0.zip",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
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40 "unite8.0_euka": "https://files.plutof.ut.ee/public/orig/D6/96/D69658E99589D888A207805A744019DBA4EC0F603E67E53732767B3E03A5AA86.zip",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
matthias
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41 "unite8.0_euka_singletons": "https://files.plutof.ut.ee/doi/C2/20/C22034350E32D6AD7E5D1AF3F8BC487E34DA0BE25602B0E748906005CE6ADA97.zip",
0
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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42 "gg13.84":"https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1",
2
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43 "RefSeq_RDP_2018_05": "https://zenodo.org/record/2541239/files/RefSeq-RDP16S_v2_May2018.fa.gz?download=1",
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44 "gtdb_2018_11_20": "https://zenodo.org/record/2541239/files/GTDB_bac-arc_ssu_r86.fa.gz?download=1",
b4c303665291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty
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45 "hitdb1": "https://zenodo.org/record/159205/files/hitdb_v1.00.fa.gz?download=1",
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46 "silva132_euk_18S": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1",
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47 "PR2v4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz"
0
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48 }
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49
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50 FILE2SPECIESURL = {
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51 "silva132":"https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1",
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52 "silva128":"https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1",
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53 "rdp16":"https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1",
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54 "rdp14":"https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1"
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55 }
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56
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57 FILE2TAXLEVELS = {
2
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58 "PR2v4.11.1": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species"
0
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59 }
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60
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61 def url_download(url, fname, workdir):
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62 """
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63 download url to workdir/fname
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64
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65 return the path to the resulting file
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66 """
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67 file_path = os.path.join(workdir, fname)
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68 if not os.path.exists(workdir):
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69 os.makedirs(workdir)
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70 src = None
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71 dst = None
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72 try:
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73 req = Request(url)
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74 src = urlopen(req)
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75 with open(file_path, 'wb') as dst:
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76 while True:
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77 chunk = src.read(2**10)
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78 if chunk:
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79 dst.write(chunk)
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80 else:
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81 break
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82 finally:
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83 if src:
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84 src.close()
2
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85
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86 #special treatment of UNITE DBs: they are zip files containing two fasta (xyz.fasta and developer/xyz.fasta)
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87 if fname.startswith("unite"):
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88 import glob
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89 import gzip
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90 import shutil
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91 import zipfile
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92 # unzip download
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93 zip_ref = zipfile.ZipFile(file_path, 'r')
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94 zip_ref.extractall(workdir)
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95 zip_ref.close()
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96 # gzip top level fasta file
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97 fastas = glob.glob("*fasta")
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98 if len(fastas) != 1:
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99 msg = "UNITE download %s contained more than one or no fasta file"
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100 raise Exception(msg)
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101 with open(fastas[0], 'rb') as f_in:
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102 with gzip.open(file_path, 'wb') as f_out:
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103 shutil.copyfileobj(f_in, f_out)
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104
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105 return fname
0
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106
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107 def main(dataset, outjson):
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108
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109 params = json.loads(open(outjson).read())
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110 target_directory = params['output_data'][0]['extra_files_path']
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111 os.mkdir(target_directory)
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112 output_path = os.path.abspath(os.path.join(os.getcwd(), 'dada2'))
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113
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114 workdir = os.path.join(os.getcwd(), 'dada2')
2
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115 path = url_download( FILE2TAXURL[dataset], dataset+".taxonomy", workdir)
0
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116
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117 data_manager_json = {"data_tables":{}}
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118 data_manager_entry = {}
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119 data_manager_entry['value'] = dataset
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120 data_manager_entry['name'] = FILE2NAME[dataset]
2
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121 data_manager_entry['path'] = dataset+".taxonomy"
0
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122 data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS)
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123 data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry
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124
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125
2
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126 if FILE2SPECIESURL.get(dataset, False ):
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127 path = url_download( FILE2SPECIESURL[dataset], dataset+".species", workdir)
0
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128
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129 data_manager_entry = {}
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130 data_manager_entry['value'] = dataset
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131 data_manager_entry['name'] = FILE2NAME[dataset]
2
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132 data_manager_entry['path'] = dataset+".species"
0
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133 data_manager_json["data_tables"]["dada2_species"] = data_manager_entry
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134
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135 for filename in os.listdir(workdir):
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136 shutil.move(os.path.join(output_path, filename), target_directory)
2
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137
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138 sys.stderr.write("JSON %s" %json.dumps(data_manager_json))
0
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139 file(outjson, 'w').write(json.dumps(data_manager_json))
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140
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141 if __name__ == '__main__':
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142 parser = argparse.ArgumentParser(description='Create data manager json.')
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143 parser.add_argument('--out', action='store', help='JSON filename')
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144 parser.add_argument('--dataset', action='store', help='Download data set name')
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145 args = parser.parse_args()
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146
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147 main(args.dataset, args.out)