#!/usr/bin/env python
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
"""
from __future__ import print_function
import argparse
from basic_modules.workflow import Workflow
from utils import logger
from utils import remap
from tool.kallisto_indexer import kallistoIndexerTool
from tool.kallisto_quant import kallistoQuantificationTool
# ------------------------------------------------------------------------------
[docs]class process_rnaseq(Workflow):
"""
Functions for downloading and processing RNA-seq FastQ files. Files are
downloaded from the European Nucleotide Archive (ENA), then they are mapped
to quantify the amount of cDNA
"""
def __init__(self, configuration=None):
"""
Initialise the class
Parameters
----------
configuration : dict
a dictionary containing parameters that define how the operation
should be carried out, which are specific to each Tool.
"""
logger.info("Processing RNA-Seq")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
Main run function for processing RNA-Seq FastQ data. Pipeline aligns
the FASTQ files to the genome using Kallisto. Kallisto is then also
used for peak calling to identify levels of expression.
Parameters
----------
files_ids : dict
List of file locations (genome FASTA, FASTQ_01, FASTQ_02 (for
paired ends))
metadata : dict
Required meta data
output_files : dict
List of output file locations
Returns
-------
outputfiles : list
List of locations for the output bam, bed and tsv files
Parameters
----------
input_files : list
List of file locations
metadata : list
Required meta data
output_files : list
List of output file locations
Returns
-------
outputfiles : dict
List of locations for the output index files
output_metadata : dict
Metadata about each of the files
"""
if "cdna_public" in input_files:
input_files["cdna"] = input_files.pop("cdna_public")
metadata["cdna"] = metadata.pop("cdna_public")
if "gff_public" in input_files:
input_files["gff"] = input_files.pop("gff_public")
metadata["gff"] = metadata.pop("gff_public")
# Index the cDNA
# This could get moved to the general tools section
k_index = kallistoIndexerTool(self.configuration)
logger.progress("Kallisto Indexer", status="RUNNING")
k_out, k_meta = k_index.run(
{"cdna": input_files["cdna"]},
{"cdna": metadata["cdna"]},
{"index": output_files["index"]}
)
logger.progress("Kallisto Indexer", status="DONE")
if "index" not in k_out:
logger.fatal("Kallisto: Index has not been generated")
return {}, {}
# Quantification
k_quant = kallistoQuantificationTool()
logger.progress("Kallisto Quant", status="RUNNING")
if "fastq2" not in input_files:
kq_input_files = {
"cdna": input_files["cdna"],
"fastq1": input_files["fastq1"],
"index": k_out["index"],
"gff": input_files["gff"],
}
kq_input_meta = {
"cdna": metadata["cdna"],
"fastq1": metadata["fastq1"],
"gff": metadata["gff"],
"index": k_meta["index"]
}
kq_files, kq_meta = k_quant.run(
kq_input_files,
kq_input_meta,
remap(
output_files,
"abundance_h5_file", "abundance_tsv_file",
"abundance_gff_file", "run_info_file"
)
)
elif "fastq2" in input_files:
kq_input_files = {
"cdna": input_files["cdna"],
"fastq1": input_files["fastq1"],
"fastq2": input_files["fastq2"],
"index": k_out["index"],
"gff": input_files["gff"],
}
kq_input_meta = {
"cdna": metadata["cdna"],
"fastq1": metadata["fastq1"],
"fastq2": metadata["fastq2"],
"index": k_meta["index"],
"gff": metadata["gff"],
}
kq_files, kq_meta = k_quant.run(
kq_input_files,
kq_input_meta,
remap(
output_files,
"abundance_h5_file", "abundance_tsv_file",
"abundance_gff_file", "run_info_file")
)
logger.progress("Kallisto Quant", status="DONE")
try:
kq_files["index"] = k_out["index"]
kq_meta["index"] = k_meta["index"]
tool_name = kq_meta['index'].meta_data['tool']
kq_meta['index'].meta_data['tool_description'] = tool_name
kq_meta['index'].meta_data['tool'] = "process_rnaseq"
tool_name = kq_meta['abundance_h5_file'].meta_data['tool']
kq_meta['abundance_h5_file'].meta_data['tool_description'] = tool_name
kq_meta['abundance_h5_file'].meta_data['tool'] = "process_rnaseq"
tool_name = kq_meta['abundance_tsv_file'].meta_data['tool']
kq_meta['abundance_tsv_file'].meta_data['tool_description'] = tool_name
kq_meta['abundance_tsv_file'].meta_data['tool'] = "process_rnaseq"
tool_name = kq_meta['run_info_file'].meta_data['tool']
kq_meta['run_info_file'].meta_data['tool_description'] = tool_name
kq_meta['run_info_file'].meta_data['tool'] = "process_rnaseq"
except KeyError:
logger.fatal("Kallisto failed")
return (kq_files, kq_meta)
# -----------------------------------------------------------------------------
def main_json(config, in_metadata, out_metadata):
"""
Alternative main function
-------------
This function launches the app using configuration written in
two json files: config.json and input_metadata.json.
"""
# 1. Instantiate and launch the App
print("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
result = app.launch(process_rnaseq,
config,
in_metadata,
out_metadata)
# 2. The App has finished
print("2. Execution finished; see " + out_metadata)
print(result)
return result
# ------------------------------------------------------------------------------
if __name__ == "__main__":
# Set up the command line parameters
PARSER = argparse.ArgumentParser(
description="Parse RNA-seq for expression analysis")
PARSER.add_argument(
"--config", help="Configuration file")
PARSER.add_argument(
"--in_metadata", help="Location of input metadata file")
PARSER.add_argument(
"--out_metadata", help="Location of output metadata file")
PARSER.add_argument(
"--local", action="store_const", const=True, default=False)
# Get the matching parameters from the command line
ARGS = PARSER.parse_args()
CONFIG = ARGS.config
IN_METADATA = ARGS.in_metadata
OUT_METADATA = ARGS.out_metadata
LOCAL = ARGS.local
if LOCAL:
import sys
sys._run_from_cmdl = True # pylint: disable=protected-access
RESULTS = main_json(CONFIG, IN_METADATA, OUT_METADATA)
print(RESULTS)