diff data_manager/FROGS_data_manager.py @ 0:7403d6c4f510 draft default tip

"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/FROGS_data_manager.py	Mon Aug 23 10:21:10 2021 +0000
@@ -0,0 +1,199 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2021 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+__author__ = 'David Christiany Migale Jouy en Josas / Maria Bernard - Sigenae Jouy en Josas'
+__copyright__ = 'Copyright (C) 2020 INRAE'
+__license__ = 'GNU General Public License'
+__version__ = '3.2.3'
+__email__ = '[e-mail]'
+__status__ = 'prod'
+
+# import json
+import argparse
+import os
+# import sys
+import tarfile
+import time
+import urllib
+
+from galaxy.util.json import from_json_string, to_json_string
+
+import requests
+
+# GALAXY_database=~/galaxy/galaxy-20.09/database
+# FROGS_data_manager.py --database=frogs_db_data --all_dbs=false \
+# --date=0 --amplicons=16S --bases=SILVA --filters=Pintail100 \
+# --only_last_versions=true \
+# --tool_data=/home/maria/galaxy/galaxy-20.09/tool-data \
+# --output $GALAXY_database/objects/e/7/7/dataset_e7766c39-8f36-450c-adf5-3e4ee8d5c562.dat
+
+
+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
+
+
+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):
+    db_dict = dict()
+    for line in db_index:
+        db_type = "_".join(line[1:4]) if line[3] != "" else "_".join(line[1:3])
+        if db_type not in db_dict:
+            db_dict[db_type] = line
+    return list(db_dict.values())
+
+
+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 = decoded_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
+    if args.all_dbs == "false":
+        # filter by amplicons
+        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 base
+        if len(bases_list) != 0:
+            db_index = [line for line in db_index if line[2] in bases_list]
+        # filter by filters
+        if len(filters_list) != 0:
+            db_index = [line for line in db_index if line[3] in filters_list]
+        # filter by date
+        if bottom_date != 0:
+            db_index = [line for line in db_index if int(line[0]) >= bottom_date]
+    if args.only_last_versions == "true":
+        # keep only last version
+        db_index = keep_only_last_version(db_index)
+
+    # 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("_", " ") if "_" not in line[4] else value.replace(line[4], "").replace("_", " ") + line[4]
+        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.request.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):
+#     HVL_dir = "http://genoweb.toulouse.inra.fr/frogs_databanks/HVL/ITS/UNITE_s_7.1_20112016"
+#     os.chdir(target_directory)
+#     for link in [HVL_dir + "/Unite_s_7.1_20112016_ITS1.fasta",HVL_dir + "/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, "frogs_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, 'wt').write(to_json_string(data_manager_dict))
+
+
+if __name__ == "__main__":
+    main()