Mercurial > repos > matthias > data_manager_dada2
diff data_manager/data_manager.py @ 3:3a4ee8bf012a draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
| author | matthias |
|---|---|
| date | Tue, 09 Apr 2019 07:18:57 -0400 |
| parents | b4c303665291 |
| children |
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--- a/data_manager/data_manager.py Fri Mar 08 05:38:44 2019 -0500 +++ b/data_manager/data_manager.py Tue Apr 09 07:18:57 2019 -0400 @@ -14,55 +14,49 @@ DEFAULT_TAXLEVELS="Kingdom,Phylum,Class,Order,Family,Genus,Species" FILE2NAME = { - "silva132":"Silva version 132", - "silva128":"Silva version 128", - "rdp16":"RDP trainset 16", - "rdp14":"RDP trainset 14", - "gg13.84":"GreenGenes version 13.8", - "unite8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi", - "unite8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", - "unite8.0_euka": "UNITE: General Fasta release 8.0 for all Eukaryotes", - "unite8.0_euka_singletons": "UNITE: General Fasta release 8.0 for all Eukaryotes including global and 97% singletons", + "silva_132":"Silva version 132", + "silva_128":"Silva version 128", + "rdp_16":"RDP trainset 16", + "rdp_14":"RDP trainset 14", + "greengenes_13.84":"GreenGenes version 13.84", + "unite_8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi", + "unite_8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", "RefSeq_RDP_2018_05": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", - "gtdb_2018_11_20": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", - "hitdb1": "HitDB version 1 (Human InTestinal 16S rRNA)", - "silva132_euk_18S": "Silva version 132 Eukaryotic 18S", - "PR2v4.11.1": "Protist Ribosomal Reference database (PR2) 4.11.1" + "gtdb_2018_11": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", + "hitdb_1": "HitDB version 1 (Human InTestinal 16S rRNA)", + "silva_euk_18S_132": "Silva version 132 Eukaryotic 18S", + "PR2_4.11.1": "Protist Ribosomal Reference database (PR2) 4.11.1" } FILE2TAXURL = { - "silva132":"https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1", - "silva128":"https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1", - "rdp16":"https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1", - "rdp14":"https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1", - "unite8.0_fungi": "https://files.plutof.ut.ee/public/orig/EB/0C/EB0CCB3A871B77EA75E472D13926271076904A588D2E1C1EA5AFCF7397D48378.zip", - "unite8.0_fungi_singletons": "https://files.plutof.ut.ee/doi/06/A2/06A2C86256EED64085670EB0C54B7115F6DAC8F311C656A9CB33E386CFABA0D0.zip", - "unite8.0_euka": "https://files.plutof.ut.ee/public/orig/D6/96/D69658E99589D888A207805A744019DBA4EC0F603E67E53732767B3E03A5AA86.zip", - "unite8.0_euka_singletons": "https://files.plutof.ut.ee/doi/C2/20/C22034350E32D6AD7E5D1AF3F8BC487E34DA0BE25602B0E748906005CE6ADA97.zip", - "gg13.84":"https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1", + "silva_132":"https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1", + "silva_128":"https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1", + "rdp_16":"https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1", + "rdp_14":"https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1", + "unite_8.0_fungi": "https://files.plutof.ut.ee/public/orig/EB/0C/EB0CCB3A871B77EA75E472D13926271076904A588D2E1C1EA5AFCF7397D48378.zip", + "unite_8.0_fungi_singletons": "https://files.plutof.ut.ee/doi/06/A2/06A2C86256EED64085670EB0C54B7115F6DAC8F311C656A9CB33E386CFABA0D0.zip", + "greengenes_13.84":"https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1", "RefSeq_RDP_2018_05": "https://zenodo.org/record/2541239/files/RefSeq-RDP16S_v2_May2018.fa.gz?download=1", - "gtdb_2018_11_20": "https://zenodo.org/record/2541239/files/GTDB_bac-arc_ssu_r86.fa.gz?download=1", - "hitdb1": "https://zenodo.org/record/159205/files/hitdb_v1.00.fa.gz?download=1", - "silva132_euk_18S": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1", - "PR2v4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz" + "gtdb_2018_11": "https://zenodo.org/record/2541239/files/GTDB_bac-arc_ssu_r86.fa.gz?download=1", + "hitdb_1": "https://zenodo.org/record/159205/files/hitdb_v1.00.fa.gz?download=1", + "silva_euk_18S_132": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1", + "PR2_4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz" } FILE2SPECIESURL = { - "silva132":"https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1", - "silva128":"https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1", - "rdp16":"https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1", - "rdp14":"https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1" + "silva_132":"https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1", + "silva_128":"https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1", + "rdp_16":"https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1", + "rdp_14":"https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1" } FILE2TAXLEVELS = { - "PR2v4.11.1": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species" + "PR2_4.11.1": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species" } def url_download(url, fname, workdir): """ download url to workdir/fname - - return the path to the resulting file """ file_path = os.path.join(workdir, fname) if not os.path.exists(workdir): @@ -94,25 +88,23 @@ zip_ref.extractall(workdir) zip_ref.close() # gzip top level fasta file - fastas = glob.glob("*fasta") + fastas = glob.glob("%s/*fasta"%workdir) if len(fastas) != 1: - msg = "UNITE download %s contained more than one or no fasta file" + msg = "UNITE download %s contained %d fasta file(s): %s"%(url, len(fastas), " ".join(fastas)) raise Exception(msg) with open(fastas[0], 'rb') as f_in: with gzip.open(file_path, 'wb') as f_out: shutil.copyfileobj(f_in, f_out) - return fname -def main(dataset, outjson): +def remote_dataset(dataset, outjson): - params = json.loads(open(outjson).read()) - target_directory = params['output_data'][0]['extra_files_path'] - os.mkdir(target_directory) - output_path = os.path.abspath(os.path.join(os.getcwd(), 'dada2')) + with open(outjson) as jf: + params = json.loads(jf.read()) - workdir = os.path.join(os.getcwd(), 'dada2') - path = url_download( FILE2TAXURL[dataset], dataset+".taxonomy", workdir) + workdir = params['output_data'][0]['extra_files_path'] + os.mkdir(workdir) + url_download( FILE2TAXURL[dataset], dataset+".taxonomy", workdir) data_manager_json = {"data_tables":{}} data_manager_entry = {} @@ -122,21 +114,16 @@ data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS) data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry - if FILE2SPECIESURL.get(dataset, False ): - path = url_download( FILE2SPECIESURL[dataset], dataset+".species", workdir) - + url_download( FILE2SPECIESURL[dataset], dataset+".species", workdir) data_manager_entry = {} data_manager_entry['value'] = dataset data_manager_entry['name'] = FILE2NAME[dataset] data_manager_entry['path'] = dataset+".species" data_manager_json["data_tables"]["dada2_species"] = data_manager_entry - - for filename in os.listdir(workdir): - shutil.move(os.path.join(output_path, filename), target_directory) - sys.stderr.write("JSON %s" %json.dumps(data_manager_json)) - file(outjson, 'w').write(json.dumps(data_manager_json)) + with file(outjson, 'w') as jf: + jf.write(json.dumps(data_manager_json)) if __name__ == '__main__': parser = argparse.ArgumentParser(description='Create data manager json.') @@ -144,4 +131,4 @@ parser.add_argument('--dataset', action='store', help='Download data set name') args = parser.parse_args() - main(args.dataset, args.out) + remote_dataset(args.dataset, args.out)