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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import bioblend
import argparse
import os
import subprocess
import logging
import sys
import fnmatch
import time
import json
import re
import stat
import shutil
from bioblend.galaxy.objects import GalaxyInstance
from bioblend import galaxy
import utilities
import speciesData
"""
gga_get_data.py
Usage: $ python3 gga_get_data.py -i input_example.yml --config config.yml [OPTIONS]
"""
class GetData(speciesData.SpeciesData):
"""
Child of SpeciesData
Contains methods and attributes to copy data into the src_data subfolders of an organism
"""
def goto_species_dir(self):
"""
Go to the species directory (starting from the main dir)
:return:
"""
os.chdir(self.main_dir)
species_dir = os.path.join(self.main_dir, self.genus_species) + "/"
try:
os.chdir(species_dir)
except OSError:
logging.critical("Cannot access %s" % species_dir)
sys.exit(0)
return 1
def get_source_data_files_from_path(self):
"""
Find source data files in the parent_directory
Link data files
TODO: manage access to the "parent directory" subdirectories properly
TODO: implement search/tests for individual file paths
:return:
"""
try:
os.chdir(self.species_dir)
except OSError:
logging.critical("Cannot access " + self.species_dir)
sys.exit(0)
organism_annotation_dir = os.path.abspath("./src_data/annotation/{0}/OGS{1}".format(self.species_folder_name, self.genome_version))
organism_genome_dir = os.path.abspath("./src_data/genome/{0}/v{1}".format(self.species_folder_name, self.genome_version))
datasets_to_get = {"genome_path": self.genome_path,
"gff_path": self.gff_path,
"transcripts_path": self.transcripts_path,
"proteins_path": self.proteins_path,
"interpro_path": self.interpro_path,
"orthofinder_path": self.orthofinder_path,
"blastp_path": self.blastp_path,
"blastx_path": self.blastx_path}
genome_datasets = ["genome_path"]
annotation_datasets = ["gff_path", "transcripts_path", "proteins_path", "orthofinder_path", "interpro_path", "blastp_path", "blastx_path"]
# Where to store blast results?
search_excluded_datasets = ["interpro_path", "orthofinder_path", "blastp_path", "blastx_path"]
# These datasets will not be searched if missing in the input file
# Copy dataset in the organism src_data dir tree correct folder
for k, v in datasets_to_get.items():
if k in genome_datasets:
shutil.copyfile(os.path.abspath(v), os.path.join(organism_genome_dir, os.path.basename(v)))
logging.info("Copied {0} into {1}".format(v, organism_genome_dir))
elif k in annotation_datasets:
shutil.copyfile(os.path.abspath(v), os.path.join(organism_annotation_dir, os.path.basename(v)))
logging.info("Copied {0} into {1}".format(v, organism_annotation_dir))
else:
pass
os.chdir(self.main_dir)
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Automatic data loading in containers and interaction "
"with galaxy instances for GGA"
", following the protocol @ "
"http://gitlab.sb-roscoff.fr/abims/e-infra/gga")
parser.add_argument("input",
type=str,
help="Input file (yml)")
parser.add_argument("-v", "--verbose",
help="Increase output verbosity",
action="store_false")
parser.add_argument("--config",
type=str,
help="Config path, default to the 'config' file inside the script repository")
parser.add_argument("--main-directory",
type=str,
help="Where the stack containers will be located, defaults to working directory")
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
logging.getLogger("urllib3").setLevel(logging.WARNING)
# Parsing the config file if provided, using the default config otherwise
if not args.config:
args.config = os.path.join(os.path.dirname(os.path.realpath(sys.argv[0])), "config")
else:
args.config = os.path.abspath(args.config)
if not args.main_directory:
args.main_directory = os.getcwd()
else:
args.main_directory = os.path.abspath(args.main_directory)
sp_dict_list = utilities.parse_input(args.input)
for sp_dict in sp_dict_list:
# Creating an instance of get_data_for_current_species object
get_data_for_current_species = GetData(parameters_dictionary=sp_dict)
# Starting
logging.info("gga_load_data.py called for %s" % get_data_for_current_species.full_name)
# Setting some of the instance attributes
get_data_for_current_species.main_dir = args.main_directory
get_data_for_current_species.species_dir = os.path.join(get_data_for_current_species.main_dir,
get_data_for_current_species.genus_species +
"/")
# Parse the config yaml file
get_data_for_current_species.config = utilities.parse_config(args.config)
# Change serexec permissions in repo
try:
os.chmod("%s/serexec" % get_data_for_current_species.script_dir, 0o0777)
except PermissionError:
logging.critical("Cannot access %s, exiting" % get_data_for_current_species.script_dir)
# Load config file
get_data_for_current_species.config = utilities.parse_config(args.config)
# Retrieve datasets
logging.info("Finding and copying datasets for %s" % get_data_for_current_species.full_name)
get_data_for_current_species.get_source_data_files_from_path()
logging.info("Sucessfully copied datasets for %s" % get_data_for_current_species.full_name)
# Format fasta headers (proteins)
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# logging.info("Formatting fasta files headers %s " % get_data_for_current_species.full_name)
# get_data_for_current_species.batch_modify_fasta_headers()
# logging.info("Successfully formatted files headers %s " % get_data_for_current_species.full_name)
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logging.info("Data successfully loaded and imported for %s" % get_data_for_current_species.full_name)