Mercurial > repos > oinizan > data_manager_frogs

annotate data_manager/FROGS_data_manager.py @ 4:34192d63196e draft default tip

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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 052af90b7eee0ccaff79e64e4706a8fbdb235783-dirty"
author oinizan
date Thu, 19 Aug 2021 14:53:38 +0000
parents 04845601de8c
children
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1 #!/usr/bin/env python3
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2 # -*- coding: utf-8 -*-
1
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3 #
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4 # Copyright (C) 2021 INRA
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5 #
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6 # This program is free software: you can redistribute it and/or modify
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7 # it under the terms of the GNU General Public License as published by
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8 # the Free Software Foundation, either version 3 of the License, or
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9 # (at your option) any later version.
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10 #
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11 # This program is distributed in the hope that it will be useful,
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12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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14 # GNU General Public License for more details.
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15 #
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16 # You should have received a copy of the GNU General Public License
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17 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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18 #
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19
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20 __author__ = 'David Christiany Migale Jouy en Josas / Maria Bernard - Sigenae Jouy en Josas'
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21 __copyright__ = 'Copyright (C) 2020 INRAE'
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22 __license__ = 'GNU General Public License'
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23 __version__ = '3.2.3'
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24 __email__ = 'frogs-support@inrae.fr'
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25 __status__ = 'prod'
0
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27 # import json
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28 import argparse
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29 import os
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30 # import sys
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31 import tarfile
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32 import time
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33 import urllib
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34
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35 from galaxy.util.json import from_json_string, to_json_string
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36
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37 import requests
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38
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39 # GALAXY_database=~/galaxy/galaxy-20.09/database
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40 # FROGS_data_manager.py --database=frogs_db_data --all_dbs=false \
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41 # --date=0 --amplicons=16S --bases=SILVA --filters=Pintail100 \
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42 # --only_last_versions=true \
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43 # --tool_data=/home/maria/galaxy/galaxy-20.09/tool-data \
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44 # --output $GALAXY_database/objects/e/7/7/dataset_e7766c39-8f36-450c-adf5-3e4ee8d5c562.dat
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45
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46
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47 def get_args():
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48 parser = argparse.ArgumentParser()
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49 parser.add_argument("-d", "--database")
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50 parser.add_argument("--all_dbs")
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51 parser.add_argument("--date")
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52 parser.add_argument("--amplicons")
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53 parser.add_argument("--bases")
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54 parser.add_argument("--filters")
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55 parser.add_argument("--only_last_versions")
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56 parser.add_argument("--tool_data")
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57 parser.add_argument("-o", "--output")
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58 args = parser.parse_args()
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59
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60 return args
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61
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62
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63 def _add_data_table_entry(data_manager_dict, data_table_entry, data_table):
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64 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
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65 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, [])
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66 data_manager_dict['data_tables'][data_table].append(data_table_entry)
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67 return data_manager_dict
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68
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69
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70 def keep_only_last_version(db_index):
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71 db_dict = dict()
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72 for line in db_index:
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73 db_type = "_".join(line[1:4]) if line[3] != "" else "_".join(line[1:3])
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74 if db_type not in db_dict:
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75 db_dict[db_type] = line
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76 return list(db_dict.values())
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77
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78
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79 def frogs_sources(data_manager_dict, target_directory):
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80
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81 # variables
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82 amplicons_list = []
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83 bases_list = []
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84 filters_list = []
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85 if args.all_dbs == "false":
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86 amplicons_list = [amplicon.lower().strip() for amplicon in args.amplicons.split(",") if amplicon != ""]
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87 bases_list = [base.lower().strip() for base in args.bases.split(",") if base != ""]
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88 filters_list = [filter.lower().strip() for filter in args.filters.split(",") if filter != ""]
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89 bottom_date = int(args.date)
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90 tool_data_path = args.tool_data
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91
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92 # get frogs database index
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93 frogs_db_index_link = "http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/FROGS_databases.tsv"
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94 with requests.Session() as s:
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95 download = s.get(frogs_db_index_link)
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96 decoded_content = download.content.decode('utf-8')
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97 db_index = decoded_content.splitlines()
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98 db_index = [line.split("\t") for line in db_index[1:]]
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99 db_index = [[line[0], line[1].lower(), line[2].lower(), line[3].lower()] + line[4:] for line in db_index]
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100
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101 # filter databases
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102 if args.all_dbs == "false":
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103 # filter by amplicons
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104 if len(amplicons_list) != 0:
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105 db_index = [line for line in db_index if any([amplicon in amplicons_list for amplicon in line[1].split(',')])]
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106 # filter by base
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107 if len(bases_list) != 0:
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108 db_index = [line for line in db_index if line[2] in bases_list]
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109 # filter by filters
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110 if len(filters_list) != 0:
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111 db_index = [line for line in db_index if line[3] in filters_list]
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112 # filter by date
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113 if bottom_date != 0:
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114 db_index = [line for line in db_index if int(line[0]) >= bottom_date]
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115 if args.only_last_versions == "true":
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116 # keep only last version
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117 db_index = keep_only_last_version(db_index)
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118
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119 # get frogs dbs
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120 os.chdir(target_directory)
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121 dir_name = "frogs_db_" + time.strftime("%Y%m%d")
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122 os.mkdir(dir_name)
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123 dbs = set([])
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124 for line in db_index:
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125 value = line[5]
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126 name = value.replace("_", " ") if "_" not in line[4] else value.replace(line[4], "").replace("_", " ") + line[4]
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127 link = line[6]
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128 name_dir = "".join([line[6].replace(".tar.gz", "").split("/")[-1]])
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129 file_path = tool_data_path + "/frogs_db/" + name_dir
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130 if not os.path.exists(file_path): # if the file is not already in frogs_db directory
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131
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132 # download frogs db
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133 dl_file = urllib.request.URLopener()
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134 dl_file.retrieve(link, "tmp.tar.gz")
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135
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136 # unzip frogs db
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137 with tarfile.open("tmp.tar.gz") as tar:
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138 tar.extractall(dir_name)
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139 tar.close()
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140 os.remove('tmp.tar.gz')
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141
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142 # get fasta file path
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143 tmp = set(os.listdir(dir_name))
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144 new_db = dir_name + "/" + "".join(tmp.difference(dbs))
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145 files = os.listdir(new_db)
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146 fasta = "".join([file for file in files if file.endswith('.fasta')])
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147 path = new_db + '/' + fasta
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148 dbs = os.listdir(dir_name)
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149 # release = value + "_" + time.strftime("%Y-%m-%d")
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150 # date = time.strftime("%Y%m%d")
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151 path = os.path.join(target_directory, path)
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152
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153 data_table_entry = dict(name=name, value=value, path=path)
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154 _add_data_table_entry(data_manager_dict, data_table_entry, "frogs_db")
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155
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156 # def HVL_sources(data_manager_dict,target_directory):
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157 # HVL_dir = "http://genoweb.toulouse.inra.fr/frogs_databanks/HVL/ITS/UNITE_s_7.1_20112016"
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158 # os.chdir(target_directory)
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159 # for link in [HVL_dir + "/Unite_s_7.1_20112016_ITS1.fasta",HVL_dir + "/Unite_s_7.1_20112016_ITS2.fasta"]:
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160 # file_name=link.split("/")[-1].replace('.fasta',"_"+time.strftime("%Y-%m-%d")+".fasta")
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161 # dl_file = urllib.URLopener()
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162 # dl_file.retrieve(link,file_name)
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163
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164 # #get fasta file path
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165 # path = os.path.join(target_directory,file_name)
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166 # if link.endswith('ITS1.fasta'):
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167 # name = "UNITE 7.1 ITS1 " + time.strftime("%Y-%m-%d")
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168 # elif link.endswith('ITS2.fasta'):
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169 # name = "UNITE 7.1 ITS2 " + time.strftime("%Y-%m-%d")
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170 # value=file_name.replace('.fasta','')
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171
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172 # data_table_entry = dict(name = name, value = value, path=path)
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173 # _add_data_table_entry(data_manager_dict, data_table_entry, "frogs_HVL_db")
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174
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175
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176 def main():
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177
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178 # get args from command line
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179 global args
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180 args = get_args()
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181
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182 # Extract json file params
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183 data_manager_dict = {}
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184 filename = args.output
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185 params = from_json_string(open(filename).read())
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186 target_directory = params['output_data'][0]['extra_files_path']
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187 os.mkdir(target_directory)
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188
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189 # if args.database=="frogs_db_data":
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190 frogs_sources(data_manager_dict, target_directory)
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191 # elif args.database=="HVL_db_data":
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192 # HVL_sources(data_manager_dict,target_directory)
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193
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194 # save info to json file
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195 open(filename, 'wt').write(to_json_string(data_manager_dict))
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196
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197
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198 if __name__ == "__main__":
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199 main()