view data_manager/FROGS_data_manager.py @ 11:0cc5f020640e draft default tip

planemo upload commit b0ebe74a020dcb21b79d8d39e7b6a2f6533b2fc4-dirty

# -*- coding: utf-8 -*-
from galaxy.util.json import from_json_string, to_json_string
import os, sys, argparse, time, json, requests, urllib, tarfile

def get_args():
    parser = argparse.ArgumentParser()
    parser.add_argument("-d","--database")
    parser.add_argument("--all_dbs")
    parser.add_argument("--date")
    parser.add_argument("--amplicons")
    parser.add_argument("--bases")
    parser.add_argument("--filters")
    parser.add_argument("--only_last_versions")
    parser.add_argument("--tool_data")
    parser.add_argument("-o","--output")
    args = parser.parse_args()
    return args

#build database last version dictionary: key=base_id, value=last version
def build_last_version_dict(db_index):
    last_version_dict={}
    for line in db_index :
        date=int(line[0])
        base_id=line[5]
        if base_id in last_version_dict:
            if date > last_version_dict[base_id] : last_version_dict[base_id]=date
        else:
            last_version_dict[base_id]=date
    return(last_version_dict)

def _add_data_table_entry(data_manager_dict, data_table_entry,data_table):
    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, [])
    data_manager_dict['data_tables'][data_table].append(data_table_entry)
    return data_manager_dict

def keep_only_last_version(db_index):
    values=["_".join(line[5].split("_")[:-1]) for line in db_index]
    to_filter = list(set([val for val in values if values.count(val) >1]))
    out = [line for line in db_index if "_".join(line[5].split("_")[:-1]) not in to_filter] 
    for bd in to_filter:
        versions = [line[4] for line in db_index if "_".join(line[5].split("_")[:-1])==bd]
        to_keep = bd+"_"+sorted(versions)[-1]
        for line in db_index:
            if line[5]==to_keep:
                out.append(line)
                print(line)
                break
    return(out)

def frogs_sources(data_manager_dict,target_directory):

    #variables
    amplicons_list=[]
    bases_list=[]
    filters_list=[]
    if  args.all_dbs=="false": 
        amplicons_list = [amplicon.lower().strip() for amplicon in args.amplicons.split(",") if amplicon != ""]
        bases_list = [base.lower().strip() for base in args.bases.split(",") if base != ""]
        filters_list = [filter.lower().strip() for filter in args.filters.split(",") if filter!=""]
        bottom_date = int(args.date)
    tool_data_path=args.tool_data

    #get frogs database index
    frogs_db_index_link="http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/FROGS_databases.tsv"
    with requests.Session() as s:
        download = s.get(frogs_db_index_link)
        decoded_content = download.content.decode('utf-8')
        db_index = download.content.splitlines()    
        db_index = [line.split("\t") for line in db_index[1:]]
        db_index = [[line[0],line[1].lower(),line[2].lower(),line[3].lower()]+line[4:] for line in db_index]

    #filter databases
    last_version_dict=build_last_version_dict(db_index)
    if args.all_dbs=="false":
        if len(amplicons_list)!=0: db_index = [line for line in db_index if any([amplicon in amplicons_list for amplicon in line[1].split(',')])]   #filter by amplicons
        if len(bases_list)!=0: db_index = [line for line in db_index if line[2] in bases_list]                                                      #filter by base
        if len(filters_list)!=0: db_index = [line for line in db_index if line[3] in filters_list]                                                  #filter by filters
        if bottom_date!=0: db_index = [line for line in db_index if int(line[0])>=bottom_date]                                                      #filter by date
    if args.only_last_versions=="true":
        db_index = keep_only_last_version(db_index)                                                          #keep only last version

    #get frogs dbs
    os.chdir(target_directory)
    dir_name="frogs_db_"+time.strftime("%Y%m%d")
    os.mkdir(dir_name)
    dbs=set([])
    for line in db_index:
        value=line[5]
        name=value.replace("_"," ")
        link=line[6]
        name_dir="".join([line[6].replace(".tar.gz","").split("/")[-1]])
        file_path=tool_data_path+"/frogs_db/"+name_dir
        if not os.path.exists(file_path):   #if the file is not already in frogs_db directory
            
            #download frogs db
            dl_file = urllib.URLopener()
            dl_file.retrieve(link, "tmp.tar.gz")
            
            #unzip frogs db
            with tarfile.open("tmp.tar.gz") as tar:
                tar.extractall(dir_name)
                tar.close()
                os.remove('tmp.tar.gz')
            
            #get fasta file path
            tmp = set(os.listdir(dir_name))
            new_db = dir_name+"/"+"".join(tmp.difference(dbs))
            files = os.listdir(new_db)
            fasta = "".join([file for file in files if file.endswith('.fasta')])
            path = new_db+'/'+fasta
            dbs = os.listdir(dir_name)
            release = value+"_"+time.strftime("%Y-%m-%d")
            date=time.strftime("%Y%m%d")
            path = os.path.join(target_directory,path)

            data_table_entry = dict(name = name, value = value, path=path)
            _add_data_table_entry(data_manager_dict, data_table_entry, "frogs_db")

def HVL_sources(data_manager_dict,target_directory):

    #get phiX files
    os.chdir(target_directory)
    for link in ["http://genoweb.toulouse.inra.fr/frogs_databanks/HVL/ITS/UNITE_s_7.1_20112016/Unite_s_7.1_20112016_ITS1.fasta","http://genoweb.toulouse.inra.fr/frogs_databanks/HVL/ITS/UNITE_s_7.1_20112016/Unite_s_7.1_20112016_ITS2.fasta"]:
        file_name=link.split("/")[-1].replace('.fasta',"_"+time.strftime("%Y-%m-%d")+".fasta")
        dl_file = urllib.URLopener()
        dl_file.retrieve(link,file_name)

        #get fasta file path
        path = os.path.join(target_directory,file_name)
        if link.endswith('ITS1.fasta'):
            name = "UNITE 7.1 ITS1 " + time.strftime("%Y-%m-%d")
        elif link.endswith('ITS2.fasta'):
            name = "UNITE 7.1 ITS2 " + time.strftime("%Y-%m-%d")
        value=file_name.replace('.fasta','')

        data_table_entry = dict(name = name, value = value, path=path)
        _add_data_table_entry(data_manager_dict, data_table_entry, "HVL_db")

def main():

    #get args from command line
    global args
    args = get_args()

    # Extract json file params
    data_manager_dict = {}
    filename = args.output
    params = from_json_string(open(filename).read())
    target_directory = params[ 'output_data' ][0]['extra_files_path']
    os.mkdir(target_directory)

    if args.database=="frogs_db_data":
        frogs_sources(data_manager_dict,target_directory)
    elif args.database=="HVL_db_data":
        HVL_sources(data_manager_dict,target_directory)

    #save info to json file
    open(filename, 'wb').write(to_json_string(data_manager_dict))

if __name__ == "__main__":
    main()