#!/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 CHiC.tool.hicup_tool import hicup
################################################
[docs]class process_hicup(Workflow):
"""
This class run hicup tool which run hicup, doing the alignment and
filtering of the reads and convert them into a BAM file.
"""
def __init__(self, configuration=None):
"""
initiate the class
Parameters
----------
configuration: dict
dictionary with parameters for different Tools, indicating
how to run each of them
"""
logger.info("Truncate C-HiC fastq reads")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
This is the main function that runs
Parameters
----------
input_files: dict
fastq1
fastq2
metadata: dict
output_files: dict
out_dir: str
directory to write the output
Returns
-------
results: bool
output_metadata: dict
"""
if "genome_fa_public" in input_files:
input_files["genome_fa"] = input_files.pop("genome_fa_public")
metadata["genome_fa"] = metadata.pop("genome_fa_public")
input_files["bowtie_gen_idx"] = input_files.pop("bowtie_gen_idx_public")
metadata["bowtie_gen_idx"] = metadata.pop("bowtie_gen_idx_public")
try:
hicup_caller = hicup(self.configuration)
output_files_hicup, output_metadata_hicup = hicup_caller.run(
{
"genome_fa": input_files["genome_fa"],
"fastq1": input_files["fastq1"],
"fastq2" : input_files["fastq2"],
"bowtie_gen_idx": input_files["bowtie_gen_idx"]
},
{
"genome_fa": metadata["genome_fa"],
"fastq1": metadata["fastq1"],
"fastq2": metadata["fastq2"]
},
{
"hicup_outdir_tar" : output_files["hicup_outdir_tar"]
}
)
#if os.path.isfile(output_files["fastq1_trunc"]) is True:
#if os.path.getsize(output_files["fastq1_trunc"]) > 0:
return output_files_hicup, output_metadata_hicup
except IOError:
return False
#############################################################
def main_json(config, in_metadata, out_metadata):
"""
Alternative main function
This function launch the app using the configuration written
in two json files: config_process_rmapBaitmap.json and
input_process_rmapBaitmap.json
"""
#Instantiate and lauch the app
print("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
results = app.launch(process_hicup,
config,
in_metadata,
out_metadata)
#2. The App has finished
print("2. Execution finished: see " + out_metadata)
print(results)
return results
#########################################################################
if __name__ == "__main__":
#set up the command line parameters
PARSER = argparse.ArgumentParser(
description="Pipeline to truncate fastq reads")
PARSER.add_argument("--config", help="Configuration file")
PARSER.add_argument(
"--in_metadata", help="Location of 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 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)