#!/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 [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 make_directory_tree(self):
"""
Generate the directory tree for an organism
:return:
"""
os.chdir(self.main_dir)
try:
os.chdir(self.species_dir)
except OSError as exc:
logging.critical("Cannot access %s" % self.genus_species)
sys.exit(exc)
# Creation (or updating) of the src_data directory tree
try:
os.mkdir("./src_data")
except FileExistsError:
logging.debug("'src_data' directory already exist for %s" % self.full_name)
except PermissionError as exc:
logging.critical("Insufficient permission to create src_data directory tree")
sys.exit(exc)
# List of all the directories to create in src_data
src_data_dirs_li = ["./src_data", "./src_data/annotation", "./src_data/genome", "./src_data/tracks",
"./src_data/annotation/%s" % self.species_folder_name,
"./src_data/genome/%s" % self.species_folder_name,
"./src_data/annotation/{0}/OGS{1}/".format(self.species_folder_name, self.ogs_version),
"./src_data/genome/{0}/v{1}".format(self.species_folder_name, self.genome_version)]
make_dirs(dir_paths_li=src_data_dirs_li)
# Return to main directory
os.chdir(self.main_dir)
logging.info("src_data directory tree generated for %s" % self.full_name)
def get_source_data_files_from_path(self):
"""
Find source data files and copy them into the src_data dir tree
: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.ogs_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
dataset_shortname = ""
if self.sex is not None or self.sex != "":
dataset_shortname = self.genus[0].lower() + "_" + self.species.lower() + "_" + self.sex[0].lower()
else:
dataset_shortname = self.genus[0].lower() + "_" + self.species.lower()
# Copy datasets in the organism src_data dir tree correct folder
for k, v in datasets_to_get.items():
if v: # If dataset is not present in input file, skip copy
if k in genome_datasets:
logging.info("Copying {0} ({1}) into {2}".format(k, v, organism_genome_dir))
genome_fname = "{0}_v{1}.fasta".format(dataset_shortname, self.genome_version)
try:
shutil.copyfile(os.path.abspath(v), os.path.join(organism_genome_dir, genome_fname))
except Exception as exc:
logging.warning("Could not copy {0} ({1}) - Exit Code: {2})".format(k, v, exc))
elif k in annotation_datasets:
dataset_fname = ""
if k == "gff_path":
dataset_fname = "{0}_OGS{1}.gff".format(dataset_shortname, self.genome_version)
elif k == "transcripts_path":
dataset_fname = "{0}_OGS{1}_transcripts.fasta".format(dataset_shortname, self.genome_version)
elif k == "proteins_path":
dataset_fname = "{0}_OGS{1}_proteins.fasta".format(dataset_shortname, self.genome_version)
elif k == "orthofinder_path":
dataset_fname = "{0}_OGS{1}_orthofinder.tsv".format(dataset_shortname, self.genome_version)
elif k == "interpro_path":
dataset_fname = "{0}_OGS{1}_interproscan.xml".format(dataset_shortname, self.genome_version)
elif k == "blastp_path":
dataset_fname = "{0}_OGS{1}_blastp.xml".format(dataset_shortname, self.genome_version)
elif k == "blastx_path":
dataset_fname = "{0}_OGS{1}_blastx.xml".format(dataset_shortname, self.genome_version)
logging.info("Copying {0} ({1}) into {2}".format(k, v, organism_annotation_dir))
try:
shutil.copyfile(os.path.abspath(v), os.path.join(organism_annotation_dir, dataset_fname))
except Exception as exc:
logging.warning("Could not copy {0} ({1}) - Exit Code: {2}".format(k, v, exc))
else:
pass
os.chdir(self.main_dir)
def make_dirs(dir_paths_li):
"""
Recursively create directories from a list of paths with a try-catch condition
:param dir_paths_li:
:return:
"""
created_dir_paths_li = []
for dir_path in dir_paths_li:
try:
os.mkdir(dir_path)
except FileExistsError:
logging.debug("%s directory already exists" % dir_path)
except PermissionError as exc:
logging.critical("Insufficient permission to create %s" % dir_path)
sys.exit(exc)
created_dir_paths_li.append(dir_path)
return created_dir_paths_li
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("--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)
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 +
"/")
# create src_data directory tree
get_data_for_current_species.make_directory_tree()
# 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)