# HG changeset patch # User dchristiany # Date 1572259613 14400 # Node ID 238a5328279d26e5d9192f244bbe678773cc8643 # Parent 0d9cb5c5aa357199c42e5efc52a1d473594e4636 planemo upload commit b0ebe74a020dcb21b79d8d39e7b6a2f6533b2fc4-dirty diff -r 0d9cb5c5aa35 -r 238a5328279d data_manager/FROGS_data_manager.py --- a/data_manager/FROGS_data_manager.py Mon Oct 07 10:56:23 2019 -0400 +++ b/data_manager/FROGS_data_manager.py Mon Oct 28 06:46:53 2019 -0400 @@ -5,19 +5,61 @@ def get_args(): parser = argparse.ArgumentParser() parser.add_argument("-d","--database") - parser.add_argument("--custom_db") + 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 frogs_sources(data_manager_dict,target_directory,amplicons_list): +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" @@ -26,11 +68,16 @@ 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[:4]+[line[1]+"_"+line[2]+"_"+line[3]]+[line[4]] for line in db_index] #add column name + db_index = [[line[0],line[1].lower(),line[2].lower(),line[3].lower()]+line[4:] for line in db_index] - #filter amplicons - if len(amplicons_list)!=0: - db_index = [line for line in db_index if line[4] in amplicons_list] + #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 + db_index = keep_only_last_version(db_index) #keep only last version #get frogs dbs os.chdir(target_directory) @@ -38,33 +85,36 @@ os.mkdir(dir_name) dbs=set([]) for line in db_index: - value=line[4] + value=line[5] name=value.replace("_"," ") - link=line[5] + 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) - #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") + 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): @@ -89,11 +139,8 @@ def main(): #get args from command line + global args args = get_args() - if args.database=="frogs_db_data" and args.custom_db=="true": - amplicons_list = args.amplicons.split(",") - else : - amplicons_list = [] # Extract json file params data_manager_dict = {} @@ -103,7 +150,7 @@ os.mkdir(target_directory) if args.database=="frogs_db_data": - frogs_sources(data_manager_dict,target_directory,amplicons_list) + frogs_sources(data_manager_dict,target_directory) elif args.database=="HVL_db_data": HVL_sources(data_manager_dict,target_directory) diff -r 0d9cb5c5aa35 -r 238a5328279d data_manager/FROGS_data_manager.xml --- a/data_manager/FROGS_data_manager.xml Mon Oct 07 10:56:23 2019 -0400 +++ b/data_manager/FROGS_data_manager.xml Mon Oct 28 06:46:53 2019 -0400 @@ -1,4 +1,4 @@ - + @@ -8,9 +8,16 @@ python $__tool_directory__/FROGS_data_manager.py --database="$database.database" #if $database.database=="frogs_db_data" - --custom_db="$database.db_type.custom_db" - --amplicons="$database.db_type.amplicons" + --all_dbs="$database.db_type.db" + #if $database.db_type.db=="false" + --date="$database.db_type.date" + --amplicons="$database.db_type.amplicons" + --bases="$database.db_type.bases" + --filters="$database.db_type.filters" + #end if + --only_last_versions="$database.only_last_versions" #end if + --tool_data="$__tool_data_path__" --output "$output" ]]> @@ -21,47 +28,18 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + 0|[1-2]{1}[0-9]{3}[0-1]{1}[0-9]{1}([0-2]{1}[0-9]{1}|3[0-1]{1}) + + + + diff -r 0d9cb5c5aa35 -r 238a5328279d tool-data/phiX_db.loc.sample --- a/tool-data/phiX_db.loc.sample Mon Oct 07 10:56:23 2019 -0400 +++ b/tool-data/phiX_db.loc.sample Mon Oct 28 06:46:53 2019 -0400 @@ -39,4 +39,3 @@ #-rw-rwxr-- 1 gpascal FROGS 88 16 sept. 2015 phi.fa.nin #-rw-rwxr-- 1 gpascal FROGS 1348 16 sept. 2015 phi.fa.nsq # -