amrfinderplus_data_manager_build: data_manager/data_manager_build

annotate data_manager/data_manager_build_amrfinderplus.py @ 3:dfa1eb2941b0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43

author	iuc
date	Sun, 23 Nov 2025 12:21:34 +0000
parents	a5921c09b7b7
children

rev	line source
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	1 import argparse
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	2 import json
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	3 import os
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	4 import subprocess as sp
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	5 from ftplib import FTP
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	6 from io import BytesIO
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	7 from pathlib import Path
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	8
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	9 import pandas as pd
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	10
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	11
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	12 class GetAmrFinderPlusDataManager:
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	13 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	14 Create the json file with database information for galaxy data manager
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	15 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	16
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	17 def __init__(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	18 self,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	19 amrfinderplus_database="amrfinderplus_versioned_database",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	20 db_name="amrfinderplus-db",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	21 amrfinderplus_version="latest",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	22 date_version=None,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	23 ):
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	24 self.data_table_name = amrfinderplus_database
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	25 self._db_name = db_name
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	26 self._amrfinderplus_version = amrfinderplus_version
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	27 self._amrfinderplus_date_version = date_version
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	28 self.data_table_entry = None
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	29 self.amrfinderplus_table_list = None
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	30
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	31 def get_data_table_format(self):
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	32 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	33 Skeleton of a data_table format
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	34 return: a data table formatted for json output
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	35 """
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	36 self.data_table_entry = {"data_tables": {self.data_table_name: {}}}
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	37 return self.data_table_entry
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	38
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	39 def get_data_manager(self):
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	40 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	41 Create the empty data table format and add all the information into
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	42 return: The data table with database information
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	43 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	44 self.amrfinderplus_table_list = self.get_data_table_format()
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	45 amrfinderplus_value = (
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	46 f"amrfinderplus_V{self._amrfinderplus_version}"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	47 f"_{self._amrfinderplus_date_version}"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	48 )
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	49 amrfinderplus_name = (
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	50 f"V{self._amrfinderplus_version}" f"-{self._amrfinderplus_date_version}"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	51 )
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	52 data_info = dict(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	53 value=amrfinderplus_value,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	54 name=amrfinderplus_name,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	55 db_version=self._amrfinderplus_version,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	56 path=self._db_name,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	57 )
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	58 self.amrfinderplus_table_list["data_tables"][self.data_table_name] = [data_info]
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	59 return self.amrfinderplus_table_list
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	60
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	61
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	62 class DownloadAmrFinderPlusDatabase(GetAmrFinderPlusDataManager):
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	63 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	64 Download the amrfinderplus database from the ncbi.
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	65 Make the database available with hmm and indexed files
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	66 Build the data manager infos for galaxy
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	67 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	68
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	69 def __init__(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	70 self,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	71 output_dir=Path.cwd(),
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	72 ncbi_url="ftp.ncbi.nlm.nih.gov",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	73 ftp_login="anonymous",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	74 ftp_password="anonymous",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	75 amrfinderplus_database="amrfinderplus_database",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	76 db_name="amrfinderplus-db",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	77 amrfinderplus_version="latest",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	78 json_file_path=None,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	79 date_version=None,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	80 amrfinderplus_db_path=None,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	81 test_mode=False,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	82 ):
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	83
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	84 super().__init__()
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	85 self.json_file_path = json_file_path
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	86 self._output_dir = output_dir
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	87 self._ncbi_ftp_url = ncbi_url
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	88 self._ncbi_database_path = (
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	89 "pathogen/Antimicrobial_resistance/AMRFinderPlus/database"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	90 )
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	91 self._login = ftp_login
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	92 self._password = ftp_password
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	93 self._amrfinderplus_database = amrfinderplus_database
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	94 self._db_name = db_name
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	95 self._amrfinderplus_version = amrfinderplus_version
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	96 self._amrfinderplus_date_version = date_version
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	97 self.species_list = None
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	98 self.test_mode = test_mode
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	99 self.amrfinderplus_db_path = amrfinderplus_db_path
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	100
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	101 @staticmethod
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	102 def subprocess_cmd(command, *args):
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	103 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	104 Method to call external tools with any parameters
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	105 :param command: command name from the tool used (e.g. wget or makeblastdb)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	106 :param args: free number of argument need for the command tool (e.g. -r, -P ...)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	107 :return: launch the command line from the system
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	108 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	109 cmd = [command]
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	110 [cmd.append(i) for i in args]
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	111 proc = sp.run(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	112 if proc.returncode != 0:
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	113 print(f"Error type {proc.returncode} with : \n {proc}")
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	114
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	115 def download_amrfinderplus_db(self):
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	116 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	117 Download the amrfinderplus database from the ncbi ftp server
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	118 """
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	119 self.amrfinderplus_db_path = f"{self._output_dir}/{self._db_name}"
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	120 os.makedirs(self.amrfinderplus_db_path)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	121
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	122 if self._amrfinderplus_version == "latest":
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	123 self.get_amrfinderplus_version()
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	124
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	125 amrfinderplus_ftp_path = (
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	126 f"ftp://{self._login}:"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	127 f"{self._password}@{self._ncbi_ftp_url}/"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	128 f"{self._ncbi_database_path}/"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	129 f"{self._amrfinderplus_version}/"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	130 f"{self._amrfinderplus_date_version}"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	131 )
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	132
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	133 if self._amrfinderplus_version == "3.12":
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	134 taxa_group_file = "taxgroup.tab"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	135 test_dna_fasta = "AMR_DNA-Escherichia"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	136 else:
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	137 taxa_group_file = "taxgroup.tsv"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	138 test_dna_fasta = "AMR_DNA-Escherichia.fa"
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	139 if self.test_mode is True:
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	140 file_list = [
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	141 test_dna_fasta,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	142 "version.txt",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	143 taxa_group_file,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	144 "database_format_version.txt",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	145 ]
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	146 output_option = "-O"
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	147 for file in file_list:
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	148 self.subprocess_cmd(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	149 "wget",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	150 "-nd",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	151 "-np",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	152 "-r",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	153 f"{amrfinderplus_ftp_path}/{file}",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	154 output_option,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	155 f"{self.amrfinderplus_db_path}/{file}",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	156 )
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	157 else:
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	158 output_option = "-P"
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	159 self.subprocess_cmd(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	160 "wget",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	161 "-nd",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	162 "-np",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	163 "-r",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	164 amrfinderplus_ftp_path,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	165 output_option,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	166 self.amrfinderplus_db_path,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	167 )
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	168
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	169 def make_hmm_profile(self):
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	170 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	171 Make the hmm profile using the AMR.LIB file previously download
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	172 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	173 hmm_file = Path(f"{self.amrfinderplus_db_path}/AMR.LIB")
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	174 if Path.exists(hmm_file) and self.test_mode is False:
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	175 self.subprocess_cmd("hmmpress", "-f", hmm_file)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	176 else:
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	177 print("hmm_file file is missing to make hmm profiles")
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	178
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	179 def extract_filelist_makeblast(self):
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	180 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	181 Extract le list of species which have file in the database
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	182 return: a filtered species list of available species in the database
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	183 """
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	184 if self._amrfinderplus_version == "3.12":
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	185 taxa_group_file = "taxgroup.tab"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	186 else:
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	187 taxa_group_file = "taxgroup.tsv"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	188 taxa_group_path = Path(f"{self.amrfinderplus_db_path}/{taxa_group_file}")
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	189 if Path.exists(taxa_group_path):
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	190 taxa_table = pd.read_table(taxa_group_path)
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	191 taxa_table.columns = [
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	192 "taxgroup",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	193 "gpipe_taxgroup",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	194 "number_of_nucl_ref_genes",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	195 ]
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	196 taxa_df = taxa_table[taxa_table.number_of_nucl_ref_genes > 0].filter(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	197 items=["taxgroup"], axis=1
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	198 )
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	199 if self.test_mode is True:
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	200 taxa_df = taxa_df[taxa_df.taxgroup == "Escherichia"].taxgroup
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	201 else:
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	202 taxa_df = taxa_df.taxgroup
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	203 self.species_list = list(taxa_df)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	204 else:
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	205 print(f"{taxa_group_file} file is missing to list available species")
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	206
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	207 def make_blastdb(self):
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	208 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	209 Index fasta file for blast
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	210 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	211 self.extract_filelist_makeblast()
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	212 if self._amrfinderplus_version == "3.12":
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	213 nucl_file_db_list = [
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	214 f"{self.amrfinderplus_db_path}/AMR_DNA-{specie}"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	215 for specie in self.species_list
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	216 ]
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	217 amr_dna = f"{self.amrfinderplus_db_path}/AMR_CDS"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	218 amr_prot = f"{self.amrfinderplus_db_path}/AMRProt"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	219 else:
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	220 nucl_file_db_list = [
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	221 f"{self.amrfinderplus_db_path}/AMR_DNA-{specie}.fa"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	222 for specie in self.species_list
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	223 ]
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	224 amr_dna = f"{self.amrfinderplus_db_path}/AMR_CDS.fa"
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	225 amr_prot = f"{self.amrfinderplus_db_path}/AMRProt.fa"
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	226 os.chdir(self.amrfinderplus_db_path)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	227 if Path(amr_dna).exists():
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	228 nucl_file_db_list.append(amr_dna)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	229 else:
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	230 print("No file AMR_CDS detected for indexing")
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	231 if Path(amr_prot).exists():
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	232 self.subprocess_cmd("makeblastdb", "-in", amr_prot, "-dbtype", "prot")
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	233 else:
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	234 print("No file AMRProt detected for indexing")
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	235 [
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	236 self.subprocess_cmd("makeblastdb", "-in", file, "-dbtype", "nucl")
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	237 for file in nucl_file_db_list
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	238 ]
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	239
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	240 def get_amrfinderplus_version(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	241 self,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	242 version_file="version.txt",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	243 database_version_file="database_format_version.txt",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	244 ):
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	245 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	246 Check the version when latest if provided and update the number
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	247 param version_file: name of the file containing version information
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	248 param database_version_file: name of the file containing date version information
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	249 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	250 ftp = FTP(self._ncbi_ftp_url)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	251 ftp.login(self._login, self._password)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	252 ftp.cwd(f"{self._ncbi_database_path}/{self._amrfinderplus_version}")
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	253 db_version = BytesIO()
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	254 db_date_version = BytesIO()
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	255 ftp.retrbinary(f"RETR {version_file}", db_version.write)
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	256 ftp.retrbinary(f"RETR {database_version_file}", db_date_version.write)
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	257 self._amrfinderplus_date_version = (
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	258 db_version.getvalue().decode("utf-8").splitlines()[0]
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	259 )
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	260 self._amrfinderplus_version = ".".join(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	261 db_date_version.getvalue().decode("utf-8").splitlines()[0].split(".")[:2]
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	262 )
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	263
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	264 def read_json_input_file(self):
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	265 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	266 Import the json file
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	267 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	268 with open(self.json_file_path) as fh:
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	269 params = json.load(fh)
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	270 target_dir = params["output_data"][0]["extra_files_path"]
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	271 os.makedirs(target_dir)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	272 self._output_dir = target_dir
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	273
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	274 def write_json_infos(self):
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	275 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	276 Write in the imported json file
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	277 """
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	278 with open(self.json_file_path, "w") as fh:
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	279 json.dump(self.get_data_manager(), fh, sort_keys=True)
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	280
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	281
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	282 def parse_arguments():
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	283 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	284 List of arguments provided by the user
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	285 return: parsed arguments
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	286 """
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	287 # parse options and arguments
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	288 arg_parser = argparse.ArgumentParser()
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	289 arg_parser.add_argument("data_manager_json", help="json file from galaxy")
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	290 arg_parser.add_argument(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	291 "--db_version",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	292 default="latest",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	293 help="select the major version of the database (e.g. 3.10, 3.8), default is latest",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	294 )
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	295 arg_parser.add_argument(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	296 "--db_date",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	297 help="select the date into the database version (e.g. 2022-10-11.2)",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	298 )
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	299 arg_parser.add_argument(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	300 "--test",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	301 action="store_true",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	302 help="option to test the script with an lighted database",
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	303 )
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	304 return arg_parser.parse_args()
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	305
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	306
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	307 def main():
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	308 all_args = parse_arguments()
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	309 amrfinderplus_download = DownloadAmrFinderPlusDatabase(
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	310 amrfinderplus_version=all_args.db_version,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	311 date_version=all_args.db_date,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	312 json_file_path=all_args.data_manager_json,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	313 test_mode=all_args.test,
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	314 )
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	315 amrfinderplus_download.read_json_input_file()
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	316 amrfinderplus_download.download_amrfinderplus_db()
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	317 amrfinderplus_download.make_hmm_profile()
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	318 amrfinderplus_download.make_blastdb()
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	319 amrfinderplus_download.write_json_infos()
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	320
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	321
3 dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43 iuc parents: 2 diff changeset	322 if __name__ == "__main__":
0 eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19 iuc parents: diff changeset	323 main()

Mercurial > repos > iuc > amrfinderplus_data_manager_build

annotate data_manager/data_manager_build_amrfinderplus.py @ 3:dfa1eb2941b0 draft default tip