#!/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 batch_modify_fasta_headers(self):
"""
Change the fasta headers before integration, so that the indexing tool in galaxy interprets the headers
correctly and doesn't throw an error
The function will use the class attribute "source_datasets", pointing to files in the galaxy
library to find the fasta files that need their headers formatted
:return:
"""
proteins_file = None
proteins_outfile = None
annotation_dir = None
organism_annotation_dir = os.path.abspath("./src_data/annotation/{0}/OGS{1}".format(self.species_folder_name, self.ogs_version))
self.goto_species_dir()
for d in [i[0] for i in os.walk(os.getcwd() + "/src_data")]:
if "annotation" in d and self.species_folder_name in d and self.ogs_version in d:
for f in os.listdir(d):
if "proteins" in f:
proteins_file = os.path.join(d, f)
proteins_outfile = os.path.join(d, "outfile_proteins.fa")
annotation_dir = os.path.abspath(d)
# Formatting the headers
if proteins_file is not None:
self.format_fasta_headers(infile=proteins_file,
outfile=proteins_outfile,
pattern="^>mRNA",
repl=">protein")
if os.path.exists(annotation_dir + "/outfile_proteins.fa"):
subprocess.call(["mv", annotation_dir + "/outfile_proteins.fa", proteins_file],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=annotation_dir)
subprocess.call(["rm", annotation_dir + "/outfile_proteins.fa"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=annotation_dir)
else:
logging.warning("Skipping proteins fasta headers formatting (FileNotFound)")
@staticmethod
def format_fasta_headers(infile, outfile, pattern, repl):
"""
Format the fasta headers of a given file, given a matching pattern and a replacement string
:param infile:
:param outfile:
:param pattern:
:param repl:
:return:
"""
infile = open(infile, 'r')
outfile = open(outfile, 'w')
lines = infile.readlines()
for line in lines:
line_out = re.sub(pattern, repl, line)
outfile.write(line_out)
infile.close()
outfile.close()
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
# Automatically find the "main" genome and annotation datasets (genome, transcripts, proteome, gff)
# Triggers when a dataset path is empty
# Exits after a single iteration to not replicate the search
# This is VERY specific to phaeoexplorer, as the search depends on how the folders and datasets are named
for k, v in datasets_to_get.items():
if k not in search_excluded_datasets and v == "":
print("Dataset not specified (%s), searching datasets" % k)
self.find_dataset_from_source_data_parent_dir()
break
# 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)
def find_dataset_from_source_data_parent_dir(self):
"""
"Fail case" func if a dataset isn't specified in the input file. This func will search the specified "parent directory" for files matching
the current species
Highly specific to the phaeoexplorer project!
Doesn't work for interpro, orthofinder and blast datasets at the moment, those absolutely need to be written in the input file
:return
"""
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))
for dirpath, dirnames, files in os.walk(self.source_data_dir):
if self.genus_upper and self.species in str(dirpath):
for f in files:
if "Contaminants" not in str(f):
try:
if fnmatch.fnmatch(f, "*" + self.species[1:] + "_" + self.sex.upper() + ".fa"):
logging.info("Genome assembly file found - " + str(f))
self.genome_path = os.path.abspath(f)
elif fnmatch.fnmatch(f, "*" + self.species[1:] + "_" + self.sex.upper() + ".gff"):
logging.info("GFF file - " + str(f))
self.gff_path = os.path.abspath(f)
elif fnmatch.fnmatch(f, "*" + self.species[1:] + "_" + self.sex.upper() + "_transcripts-gff.fa"):
logging.info("Transcripts file - " + str(f))
self.transcripts_path = os.path.abspath(f)
elif fnmatch.fnmatch(f, "*" + self.species[1:] + "_" + self.sex.upper() + "_proteins.fa"):
logging.info("Proteins file - " + str(f))
self.proteins_path = os.path.abspath(f)
except Exception as exc:
logging.debug("Error raised %s" % exc)
def generate_blast_banks(self):
"""
TODO
Do we need to generate blast banks?
:return:
"""
return 0
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)
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)
logging.info("Data successfully loaded and imported for %s" % get_data_for_current_species.full_name)