view data_manager/data_manager.py @ 2:b4c303665291 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty

import argparse
import json
import os
import shutil
import sys
import zipfile
try:
    # For Python 3.0 and later
    from urllib.request import Request, urlopen
except ImportError:
    # Fall back to Python 2 imports
    from urllib2 import Request, urlopen

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",
    "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"
}

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",
    "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"
}

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"
}

FILE2TAXLEVELS = {
    "PR2v4.11.1": "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):
        os.makedirs(workdir)
    src = None
    dst = None
    try:
        req = Request(url)
        src = urlopen(req)
        with open(file_path, 'wb') as dst:
            while True:
                chunk = src.read(2**10)
                if chunk:
                    dst.write(chunk)
                else:
                    break
    finally:
        if src:
            src.close()

    #special treatment of UNITE DBs: they are zip files containing two fasta (xyz.fasta and developer/xyz.fasta)
    if fname.startswith("unite"):
        import glob
        import gzip
        import shutil
        import zipfile
        # unzip download
        zip_ref = zipfile.ZipFile(file_path, 'r')
        zip_ref.extractall(workdir)
        zip_ref.close()
        # gzip top level fasta file
        fastas = glob.glob("*fasta")
        if len(fastas) != 1:
            msg = "UNITE download %s contained more than one or no fasta file"
            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):

    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'))

    workdir = os.path.join(os.getcwd(), 'dada2') 
    path = url_download( FILE2TAXURL[dataset], dataset+".taxonomy", workdir)

    data_manager_json = {"data_tables":{}}
    data_manager_entry = {}
    data_manager_entry['value'] = dataset
    data_manager_entry['name'] = FILE2NAME[dataset]
    data_manager_entry['path'] = dataset+".taxonomy"
    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)
    
        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))

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Create data manager json.')
    parser.add_argument('--out', action='store', help='JSON filename')
    parser.add_argument('--dataset', action='store', help='Download data set name')
    args = parser.parse_args()

    main(args.dataset, args.out)